4WRA

Complex of 70S ribosome with tRNA-Tyr and mRNA with A-A mismatch in the first position in the A-site and with antibiotic paromomycin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural insights into the translational infidelity mechanism.

Rozov, A.Demeshkina, N.Westhof, E.Yusupov, M.Yusupova, G.

(2015) Nat Commun 6: 7251-7251

  • DOI: 10.1038/ncomms8251
  • Primary Citation of Related Structures:  
    4WQ1, 4WRA, 4WQR, 4WR6, 4WSM, 4WSD, 4WRO, 4WU1, 4WT1, 4WZO

  • PubMed Abstract: 
  • The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of missense errors during translation ...

    The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of missense errors during translation. We determined ribosome structures in rare states where incorrect tRNAs were incorporated into the peptidyl-tRNA-binding site. These structures show that in the codon-anticodon duplex, a G·U mismatch adopts the Watson-Crick geometry, indicating a shift in the tautomeric equilibrium or ionization of the nucleobase. Additional structures with mismatches in the 70S decoding centre show that the binding of any tRNA induces identical rearrangements in the centre, which favours either isosteric or close to the Watson-Crick geometry codon-anticodon pairs. Overall, the results suggest that a mismatch escapes discrimination by preserving the shape of a Watson-Crick pair and indicate that geometric selection via tautomerism or ionization dominates the translational infidelity mechanism.


    Organizational Affiliation

    Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg; CNRS, UMR7104; INSERM, U964, Illkirch 67400, France.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2DB [auth 12], B [auth 1E]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3EB [auth 22], C [auth 2E]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4FB [auth 32], D [auth 3E]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5GB [auth 42], E [auth 4E]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6HB [auth 52], F [auth 5E]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7IB [auth 62], G [auth 6E]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8JB [auth 72], H [auth 7E]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9KB [auth 82], I [auth 8E]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10LB [auth 1A], J [auth 1I]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11MB [auth 2A], K [auth 2I]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12NB [auth 3A], L [auth 3I]132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13OB [auth 4A], M [auth 4I]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZPB [auth 5A], N [auth 5I]61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15QB [auth 6A], O [auth 6I]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16RB [auth 7A], P [auth 7I]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17SB [auth 8A], Q [auth 8I]105Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18TB [auth 9A], R [auth 9I]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19UB [auth AA], S [auth AI]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20VB [auth BA], T [auth BI]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxWB [auth 1B], U [auth 1F]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2BA [auth 11], DC [auth 19]276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth 21], EC [auth 29]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4DA [auth 31], FC [auth 39]210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5EA [auth 41], GC [auth 49]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth 51], HC [auth 59]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
UniProt
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9GA [auth 61], IC [auth 69]148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13JC [auth 15], HA [auth 58]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
UniProt
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14KC [auth 25], IA [auth 68]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15LC [auth 35], JA [auth 78]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16MC [auth 45], KA [auth 88]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17NC [auth 55], LA [auth 98]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18OC [auth 65], MA [auth A8]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19PC [auth 75], NA [auth B8]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20QC [auth 85], OA [auth C8]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21RC [auth 95], PA [auth D8]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22SC [auth A5], QA [auth E8]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23TC [auth B5], RA [auth F8]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24UC [auth C5], SA [auth G8]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25VC [auth D5], TA [auth H8]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27WC [auth E5], UA [auth I8]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28XC [auth F5], VA [auth J8]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29YC [auth G5], WA [auth K8]72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30ZC [auth H5], XA [auth L8]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31AD [auth I5], YA [auth M8]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32BD [auth J5], ZA [auth N8]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34CD [auth L5], AB [auth P8]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35DD [auth M5], BB [auth Q8]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth 13], CB [auth 1G]1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
tRNA-TyrV [auth 1K]85Escherichia coli
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Entity ID: 23
MoleculeChainsLengthOrganismImage
tRNA-fMetW [auth 2K], YB [auth 2L]77Escherichia coli
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Entity ID: 24
MoleculeChainsLengthOrganismImage
tRNA-TyrXB [auth 1L], X [auth 3K]85Escherichia coli
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Entity ID: 25
MoleculeChainsLengthOrganismImage
mRNAY [auth 4K], AC [auth 4L]30Thermus thermophilus HB8
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Entity ID: 26
MoleculeChainsLengthOrganismImage
23S ribosomal RNABC [auth 14], Z [auth 1H]2918Thermus thermophilus HB8
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Entity ID: 27
MoleculeChainsLengthOrganismImage
5S ribosomal RNAAA [auth 16], CC [auth 1J]122Thermus thermophilus HB8
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Entity ID: 55
MoleculeChainsLengthOrganismImage
tRNA-TyrZB [auth 3L]85Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR (Subject of Investigation/LOI)
Query on PAR

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AGA [auth 1G], SI [auth 13]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

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CGA [auth 32], DGA [auth 5A], PCA [auth G8], WI [auth 3E], YVA [auth C5], ZI [auth 5I]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AAA [auth 1H] , ABA [auth 1H] , ACA [auth 16] , ADA [auth 1G] , AE [auth 13] , AEA [auth 1G] , AF [auth 13] , AFA [auth 1G] , 
AAA [auth 1H],  ABA [auth 1H],  ACA [auth 16],  ADA [auth 1G],  AE [auth 13],  AEA [auth 1G],  AF [auth 13],  AFA [auth 1G],  AG [auth 13],  AH [auth 13],  AHA [auth 14],  AI [auth 13],  AIA [auth 14],  AJ [auth 1K],  AJA [auth 14],  AK [auth 1H],  AKA [auth 14],  AL [auth 1H],  ALA [auth 14],  AM [auth 1H],  AMA [auth 14],  AN [auth 1H],  ANA [auth 14],  AO [auth 1H],  AOA [auth 14],  AP [auth 1H],  APA [auth 14],  AQ [auth 1H],  AQA [auth 14],  AR [auth 1H],  ARA [auth 14],  AS [auth 1H],  ASA [auth 14],  AT [auth 1H],  ATA [auth 14],  AU [auth 1H],  AUA [auth 14],  AV [auth 1H],  AVA [auth 14],  AW [auth 1H],  AX [auth 1H],  AY [auth 1H],  AZ [auth 1H],  BAA [auth 1H],  BBA [auth 1H],  BCA [auth 16],  BDA [auth 1G],  BE [auth 13],  BEA [auth 1G],  BF [auth 13],  BFA [auth 1G],  BG [auth 13],  BGA [auth 1G],  BH [auth 13],  BHA [auth 14],  BI [auth 13],  BIA [auth 14],  BJ [auth 2K],  BJA [auth 14],  BK [auth 1H],  BKA [auth 14],  BL [auth 1H],  BLA [auth 14],  BM [auth 1H],  BMA [auth 14],  BN [auth 1H],  BNA [auth 14],  BO [auth 1H],  BOA [auth 14],  BP [auth 1H],  BPA [auth 14],  BQ [auth 1H],  BQA [auth 14],  BR [auth 1H],  BRA [auth 14],  BS [auth 1H],  BSA [auth 14],  BT [auth 1H],  BTA [auth 14],  BU [auth 1H],  BUA [auth 14],  BV [auth 1H],  BVA [auth 14],  BW [auth 1H],  BX [auth 1H],  BY [auth 1H],  BZ [auth 1H],  CAA [auth 1H],  CBA [auth 1H],  CCA [auth 16],  CDA [auth 1G],  CE [auth 13],  CEA [auth 1G],  CF [auth 13],  CFA [auth 1G],  CG [auth 13],  CH [auth 13],  CHA [auth 14],  CI [auth 13],  CIA [auth 14],  CJ [auth 2K],  CJA [auth 14],  CK [auth 1H],  CKA [auth 14],  CL [auth 1H],  CLA [auth 14],  CM [auth 1H],  CMA [auth 14],  CN [auth 1H],  CNA [auth 14],  CO [auth 1H],  COA [auth 14],  CP [auth 1H],  CPA [auth 14],  CQ [auth 1H],  CQA [auth 14],  CR [auth 1H],  CRA [auth 14],  CS [auth 1H],  CSA [auth 14],  CT [auth 1H],  CTA [auth 14],  CU [auth 1H],  CUA [auth 14],  CV [auth 1H],  CVA [auth 14],  CW [auth 1H],  CX [auth 1H],  CY [auth 1H],  CZ [auth 1H],  DAA [auth 1H],  DBA [auth 1H],  DCA [auth 16],  DDA [auth 1G],  DE [auth 13],  DEA [auth 1G],  DF [auth 13],  DFA [auth 1G],  DG [auth 13],  DH [auth 13],  DHA [auth 14],  DI [auth 13],  DIA [auth 14],  DJ [auth 2K],  DJA [auth 14],  DK [auth 1H],  DKA [auth 14],  DL [auth 1H],  DLA [auth 14],  DM [auth 1H],  DMA [auth 14],  DN [auth 1H],  DNA [auth 14],  DO [auth 1H],  DOA [auth 14],  DP [auth 1H],  DPA [auth 14],  DQ [auth 1H],  DQA [auth 14],  DR [auth 1H],  DRA [auth 14],  DS [auth 1H],  DSA [auth 14],  DT [auth 1H],  DTA [auth 14],  DU [auth 1H],  DUA [auth 14],  DV [auth 1H],  DVA [auth 14],  DW [auth 1H],  DX [auth 1H],  DY [auth 1H],  DZ [auth 1H],  EAA [auth 1H],  EBA [auth 1H],  ECA [auth 16],  ED [auth 13],  EDA [auth 1G],  EE [auth 13],  EEA [auth 1G],  EF [auth 13],  EFA [auth 1G],  EG [auth 13],  EGA [auth 2L],  EH [auth 13],  EHA [auth 14],  EI [auth 13],  EIA [auth 14],  EJ [auth 2K],  EJA [auth 14],  EK [auth 1H],  EKA [auth 14],  EL [auth 1H],  ELA [auth 14],  EM [auth 1H],  EMA [auth 14],  EN [auth 1H],  ENA [auth 14],  EO [auth 1H],  EOA [auth 14],  EP [auth 1H],  EPA [auth 14],  EQ [auth 1H],  EQA [auth 14],  ER [auth 1H],  ERA [auth 14],  ES [auth 1H],  ESA [auth 14],  ET [auth 1H],  ETA [auth 14],  EU [auth 1H],  EUA [auth 14],  EV [auth 1H],  EVA [auth 14],  EW [auth 1H],  EX [auth 1H],  EY [auth 1H],  EZ [auth 1H],  FAA [auth 1H],  FBA [auth 1H],  FCA [auth 16],  FD [auth 13],  FDA [auth 1G],  FE [auth 13],  FEA [auth 1G],  FF [auth 13],  FFA [auth 1G],  FG [auth 13],  FGA [auth 2L],  FH [auth 13],  FHA [auth 14],  FI [auth 13],  FIA [auth 14],  FJ [auth 2K],  FJA [auth 14],  FK [auth 1H],  FKA [auth 14],  FL [auth 1H],  FLA [auth 14],  FM [auth 1H],  FMA [auth 14],  FN [auth 1H],  FNA [auth 14],  FO [auth 1H],  FOA [auth 14],  FP [auth 1H],  FPA [auth 14],  FQ [auth 1H],  FQA [auth 14],  FR [auth 1H],  FRA [auth 14],  FS [auth 1H],  FSA [auth 14],  FT [auth 1H],  FTA [auth 14],  FU [auth 1H],  FUA [auth 14],  FV [auth 1H],  FVA [auth 14],  FW [auth 1H],  FX [auth 1H],  FY [auth 1H],  FZ [auth 1H],  GAA [auth 1H],  GBA [auth 1H],  GCA [auth 16],  GD [auth 13],  GDA [auth 1G],  GE [auth 13],  GEA [auth 1G],  GF [auth 13],  GFA [auth 1G],  GG [auth 13],  GGA [auth 2L],  GH [auth 13],  GHA [auth 14],  GI [auth 13],  GIA [auth 14],  GJ [auth 2K],  GJA [auth 14],  GK [auth 1H],  GKA [auth 14],  GL [auth 1H],  GLA [auth 14],  GM [auth 1H],  GMA [auth 14],  GN [auth 1H],  GNA [auth 14],  GO [auth 1H],  GOA [auth 14],  GP [auth 1H],  GPA [auth 14],  GQ [auth 1H],  GQA [auth 14],  GR [auth 1H],  GRA [auth 14],  GS [auth 1H],  GSA [auth 14],  GT [auth 1H],  GTA [auth 14],  GU [auth 1H],  GUA [auth 14],  GV [auth 1H],  GVA [auth 14],  GW [auth 1H],  GX [auth 1H],  GY [auth 1H],  GZ [auth 1H],  HAA [auth 1H],  HBA [auth 1H],  HCA [auth 11],  HD [auth 13],  HDA [auth 1G],  HE [auth 13],  HEA [auth 1G],  HF [auth 13],  HFA [auth 1G],  HG [auth 13],  HGA [auth 2L],  HH [auth 13],  HHA [auth 14],  HI [auth 13],  HIA [auth 14],  HJ [auth 2K],  HJA [auth 14],  HK [auth 1H],  HKA [auth 14],  HL [auth 1H],  HLA [auth 14],  HM [auth 1H],  HMA [auth 14],  HN [auth 1H],  HNA [auth 14],  HO [auth 1H],  HOA [auth 14],  HP [auth 1H],  HPA [auth 14],  HQ [auth 1H],  HQA [auth 14],  HR [auth 1H],  HRA [auth 14],  HS [auth 1H],  HSA [auth 14],  HT [auth 1H],  HTA [auth 14],  HU [auth 1H],  HUA [auth 14],  HV [auth 1H],  HVA [auth 14],  HW [auth 1H],  HX [auth 1H],  HY [auth 1H],  HZ [auth 1H],  IAA [auth 1H],  IBA [auth 1H],  ICA [auth 11],  ID [auth 13],  IDA [auth 1G],  IE [auth 13],  IEA [auth 1G],  IF [auth 13],  IFA [auth 1G],  IG [auth 13],  IGA [auth 14],  IH [auth 13],  IHA [auth 14],  II [auth 13],  IIA [auth 14],  IJ [auth 1H],  IJA [auth 14],  IK [auth 1H],  IKA [auth 14],  IL [auth 1H],  ILA [auth 14],  IM [auth 1H],  IMA [auth 14],  IN [auth 1H],  INA [auth 14],  IO [auth 1H],  IOA [auth 14],  IP [auth 1H],  IPA [auth 14],  IQ [auth 1H],  IQA [auth 14],  IR [auth 1H],  IRA [auth 14],  IS [auth 1H],  ISA [auth 14],  IT [auth 1H],  ITA [auth 14],  IU [auth 1H],  IUA [auth 14],  IV [auth 1H],  IVA [auth 14],  IW [auth 1H],  IX [auth 1H],  IY [auth 1H],  IZ [auth 1H],  JAA [auth 1H],  JBA [auth 1H],  JCA [auth 21],  JD [auth 13],  JDA [auth 1G],  JE [auth 13],  JEA [auth 1G],  JF [auth 13],  JFA [auth 1G],  JG [auth 13],  JGA [auth 14],  JH [auth 13],  JHA [auth 14],  JI [auth 13],  JIA [auth 14],  JJ [auth 1H],  JJA [auth 14],  JK [auth 1H],  JKA [auth 14],  JL [auth 1H],  JLA [auth 14],  JM [auth 1H],  JMA [auth 14],  JN [auth 1H],  JNA [auth 14],  JO [auth 1H],  JOA [auth 14],  JP [auth 1H],  JPA [auth 14],  JQ [auth 1H],  JQA [auth 14],  JR [auth 1H],  JRA [auth 14],  JS [auth 1H],  JSA [auth 14],  JT [auth 1H],  JTA [auth 14],  JU [auth 1H],  JUA [auth 14],  JV [auth 1H],  JVA [auth 1J],  JW [auth 1H],  JX [auth 1H],  JY [auth 1H],  JZ [auth 1H],  KAA [auth 1H],  KBA [auth 1H],  KCA [auth 21],  KD [auth 13],  KDA [auth 1G],  KE [auth 13],  KEA [auth 1G],  KF [auth 13],  KFA [auth 1G],  KG [auth 13],  KGA [auth 14],  KH [auth 13],  KHA [auth 14],  KI [auth 13],  KIA [auth 14],  KJ [auth 1H],  KJA [auth 14],  KK [auth 1H],  KKA [auth 14],  KL [auth 1H],  KLA [auth 14],  KM [auth 1H],  KMA [auth 14],  KN [auth 1H],  KNA [auth 14],  KO [auth 1H],  KOA [auth 14],  KP [auth 1H],  KPA [auth 14],  KQ [auth 1H],  KQA [auth 14],  KR [auth 1H],  KRA [auth 14],  KS [auth 1H],  KSA [auth 14],  KT [auth 1H],  KTA [auth 14],  KU [auth 1H],  KUA [auth 14],  KV [auth 1H],  KVA [auth 1J],  KW [auth 1H],  KX [auth 1H],  KY [auth 1H],  KZ [auth 1H],  LAA [auth 1H],  LBA [auth 1H],  LCA [auth 31],  LD [auth 13],  LDA [auth 1G],  LE [auth 13],  LEA [auth 1G],  LF [auth 13],  LFA [auth 1G],  LG [auth 13],  LGA [auth 14],  LH [auth 13],  LHA [auth 14],  LI [auth 13],  LIA [auth 14],  LJ [auth 1H],  LJA [auth 14],  LK [auth 1H],  LKA [auth 14],  LL [auth 1H],  LLA [auth 14],  LM [auth 1H],  LMA [auth 14],  LN [auth 1H],  LNA [auth 14],  LO [auth 1H],  LOA [auth 14],  LP [auth 1H],  LPA [auth 14],  LQ [auth 1H],  LQA [auth 14],  LR [auth 1H],  LRA [auth 14],  LS [auth 1H],  LSA [auth 14],  LT [auth 1H],  LTA [auth 14],  LU [auth 1H],  LUA [auth 14],  LV [auth 1H],  LVA [auth 1J],  LW [auth 1H],  LX [auth 1H],  LY [auth 1H],  LZ [auth 1H],  MAA [auth 1H],  MBA [auth 1H],  MCA [auth 41],  MD [auth 13],  MDA [auth 1G],  ME [auth 13],  MEA [auth 1G],  MF [auth 13],  MFA [auth 1G],  MG [auth 13],  MGA [auth 14],  MH [auth 13],  MHA [auth 14],  MI [auth 13],  MIA [auth 14],  MJ [auth 1H],  MJA [auth 14],  MK [auth 1H],  MKA [auth 14],  ML [auth 1H],  MLA [auth 14],  MM [auth 1H],  MMA [auth 14],  MN [auth 1H],  MNA [auth 14],  MO [auth 1H],  MOA [auth 14],  MP [auth 1H],  MPA [auth 14],  MQ [auth 1H],  MQA [auth 14],  MR [auth 1H],  MRA [auth 14],  MS [auth 1H],  MSA [auth 14],  MT [auth 1H],  MTA [auth 14],  MU [auth 1H],  MUA [auth 14],  MV [auth 1H],  MVA [auth 1J],  MW [auth 1H],  MX [auth 1H],  MY [auth 1H],  MZ [auth 1H],  NAA [auth 1H],  NBA [auth 1H],  NCA [auth 78],  ND [auth 13],  NDA [auth 1G],  NE [auth 13],  NEA [auth 1G],  NF [auth 13],  NFA [auth 1G],  NG [auth 13],  NGA [auth 14],  NH [auth 13],  NHA [auth 14],  NI [auth 13],  NIA [auth 14],  NJ [auth 1H],  NJA [auth 14],  NK [auth 1H],  NKA [auth 14],  NL [auth 1H],  NLA [auth 14],  NM [auth 1H],  NMA [auth 14],  NN [auth 1H],  NNA [auth 14],  NO [auth 1H],  NOA [auth 14],  NP [auth 1H],  NPA [auth 14],  NQ [auth 1H],  NQA [auth 14],  NR [auth 1H],  NRA [auth 14],  NS [auth 1H],  NSA [auth 14],  NT [auth 1H],  NTA [auth 14],  NU [auth 1H],  NUA [auth 14],  NV [auth 1H],  NVA [auth 1J],  NW [auth 1H],  NX [auth 1H],  NY [auth 1H],  NZ [auth 1H],  OAA [auth 1H],  OBA [auth 1H],  OCA [auth 88],  OD [auth 13],  ODA [auth 1G],  OE [auth 13],  OEA [auth 1G],  OF [auth 13],  OFA [auth 1G],  OG [auth 13],  OGA [auth 14],  OH [auth 13],  OHA [auth 14],  OI [auth 13],  OIA [auth 14],  OJ [auth 1H],  OJA [auth 14],  OK [auth 1H],  OKA [auth 14],  OL [auth 1H],  OLA [auth 14],  OM [auth 1H],  OMA [auth 14],  ON [auth 1H],  ONA [auth 14],  OO [auth 1H],  OOA [auth 14],  OP [auth 1H],  OPA [auth 14],  OQ [auth 1H],  OQA [auth 14],  OR [auth 1H],  ORA [auth 14],  OS [auth 1H],  OSA [auth 14],  OT [auth 1H],  OTA [auth 14],  OU [auth 1H],  OUA [auth 14],  OV [auth 1H],  OVA [auth 1J],  OW [auth 1H],  OX [auth 1H],  OY [auth 1H],  OZ [auth 1H],  PAA [auth 1H],  PBA [auth 1H],  PD [auth 13],  PDA [auth 1G],  PE [auth 13],  PEA [auth 1G],  PF [auth 13],  PFA [auth 1G],  PG [auth 13],  PGA [auth 14],  PH [auth 13],  PHA [auth 14],  PI [auth 13],  PIA [auth 14],  PJ [auth 1H],  PJA [auth 14],  PK [auth 1H],  PKA [auth 14],  PL [auth 1H],  PLA [auth 14],  PM [auth 1H],  PMA [auth 14],  PN [auth 1H],  PNA [auth 14],  PO [auth 1H],  POA [auth 14],  PP [auth 1H],  PPA [auth 14],  PQ [auth 1H],  PQA [auth 14],  PR [auth 1H],  PRA [auth 14],  PS [auth 1H],  PSA [auth 14],  PT [auth 1H],  PTA [auth 14],  PU [auth 1H],  PUA [auth 14],  PV [auth 1H],  PVA [auth 29],  PW [auth 1H],  PX [auth 1H],  PY [auth 1H],  PZ [auth 1H],  QAA [auth 1H],  QBA [auth 1H],  QCA [auth I8],  QD [auth 13],  QDA [auth 1G],  QE [auth 13],  QEA [auth 1G],  QF [auth 13],  QFA [auth 1G],  QG [auth 13],  QGA [auth 14],  QH [auth 13],  QHA [auth 14],  QI [auth 13],  QIA [auth 14],  QJ [auth 1H],  QJA [auth 14],  QK [auth 1H],  QKA [auth 14],  QL [auth 1H],  QLA [auth 14],  QM [auth 1H],  QMA [auth 14],  QN [auth 1H],  QNA [auth 14],  QO [auth 1H],  QOA [auth 14],  QP [auth 1H],  QPA [auth 14],  QQ [auth 1H],  QQA [auth 14],  QR [auth 1H],  QRA [auth 14],  QS [auth 1H],  QSA [auth 14],  QT [auth 1H],  QTA [auth 14],  QU [auth 1H],  QUA [auth 14],  QV [auth 1H],  QVA [auth 29],  QW [auth 1H],  QX [auth 1H],  QY [auth 1H],  QZ [auth 1H],  RAA [auth 1H],  RBA [auth 1H],  RCA [auth L8],  RD [auth 13],  RDA [auth 1G],  RE [auth 13],  REA [auth 1G],  RF [auth 13],  RFA [auth 1G],  RG [auth 13],  RGA [auth 14],  RH [auth 13],  RHA [auth 14],  RI [auth 13],  RIA [auth 14],  RJ [auth 1H],  RJA [auth 14],  RK [auth 1H],  RKA [auth 14],  RL [auth 1H],  RLA [auth 14],  RM [auth 1H],  RMA [auth 14],  RN [auth 1H],  RNA [auth 14],  RO [auth 1H],  ROA [auth 14],  RP [auth 1H],  RPA [auth 14],  RQ [auth 1H],  RQA [auth 14],  RR [auth 1H],  RRA [auth 14],  RS [auth 1H],  RSA [auth 14],  RT [auth 1H],  RTA [auth 14],  RU [auth 1H],  RUA [auth 14],  RV [auth 1H],  RVA [auth 29],  RW [auth 1H],  RX [auth 1H],  RY [auth 1H],  RZ [auth 1H],  SAA [auth 1H],  SBA [auth 1H],  SCA [auth P8],  SD [auth 13],  SDA [auth 1G],  SE [auth 13],  SEA [auth 1G],  SF [auth 13],  SFA [auth 1G],  SG [auth 13],  SGA [auth 14],  SH [auth 13],  SHA [auth 14],  SIA [auth 14],  SJ [auth 1H],  SJA [auth 14],  SK [auth 1H],  SKA [auth 14],  SL [auth 1H],  SLA [auth 14],  SM [auth 1H],  SMA [auth 14],  SN [auth 1H],  SNA [auth 14],  SO [auth 1H],  SOA [auth 14],  SP [auth 1H],  SPA [auth 14],  SQ [auth 1H],  SQA [auth 14],  SR [auth 1H],  SRA [auth 14],  SS [auth 1H],  SSA [auth 14],  ST [auth 1H],  STA [auth 14],  SU [auth 1H],  SUA [auth 14],  SV [auth 1H],  SVA [auth 39],  SW [auth 1H],  SX [auth 1H],  SY [auth 1H],  SZ [auth 1H],  TAA [auth 1H],  TBA [auth 1H],  TCA [auth 1G],  TD [auth 13],  TDA [auth 1G],  TE [auth 13],  TEA [auth 1G],  TF [auth 13],  TFA [auth 1G],  TG [auth 13],  TGA [auth 14],  TH [auth 13],  THA [auth 14],  TI [auth 13],  TIA [auth 14],  TJ [auth 1H],  TJA [auth 14],  TK [auth 1H],  TKA [auth 14],  TL [auth 1H],  TLA [auth 14],  TM [auth 1H],  TMA [auth 14],  TN [auth 1H],  TNA [auth 14],  TO [auth 1H],  TOA [auth 14],  TP [auth 1H],  TPA [auth 14],  TQ [auth 1H],  TQA [auth 14],  TR [auth 1H],  TRA [auth 14],  TS [auth 1H],  TSA [auth 14],  TT [auth 1H],  TTA [auth 14],  TU [auth 1H],  TUA [auth 14],  TV [auth 1H],  TVA [auth 25],  TW [auth 1H],  TX [auth 1H],  TY [auth 1H],  TZ [auth 1H],  UAA [auth 1H],  UBA [auth 1H],  UCA [auth 1G],  UD [auth 13],  UDA [auth 1G],  UE [auth 13],  UEA [auth 1G],  UF [auth 13],  UFA [auth 1G],  UG [auth 13],  UGA [auth 14],  UH [auth 13],  UHA [auth 14],  UI [auth 13],  UIA [auth 14],  UJ [auth 1H],  UJA [auth 14],  UK [auth 1H],  UKA [auth 14],  UL [auth 1H],  ULA [auth 14],  UM [auth 1H],  UMA [auth 14],  UN [auth 1H],  UNA [auth 14],  UO [auth 1H],  UOA [auth 14],  UP [auth 1H],  UPA [auth 14],  UQ [auth 1H],  UQA [auth 14],  UR [auth 1H],  URA [auth 14],  US [auth 1H],  USA [auth 14],  UT [auth 1H],  UTA [auth 14],  UU [auth 1H],  UUA [auth 14],  UV [auth 1H],  UVA [auth 35],  UW [auth 1H],  UX [auth 1H],  UY [auth 1H],  UZ [auth 1H],  VAA [auth 1H],  VBA [auth 16],  VCA [auth 1G],  VD [auth 13],  VDA [auth 1G],  VE [auth 13],  VEA [auth 1G],  VF [auth 13],  VFA [auth 1G],  VG [auth 13],  VGA [auth 14],  VH [auth 13],  VHA [auth 14],  VI [auth 3E],  VIA [auth 14],  VJ [auth 1H],  VJA [auth 14],  VK [auth 1H],  VKA [auth 14],  VL [auth 1H],  VLA [auth 14],  VM [auth 1H],  VMA [auth 14],  VN [auth 1H],  VNA [auth 14],  VO [auth 1H],  VOA [auth 14],  VP [auth 1H],  VPA [auth 14],  VQ [auth 1H],  VQA [auth 14],  VR [auth 1H],  VRA [auth 14],  VS [auth 1H],  VSA [auth 14],  VT [auth 1H],  VTA [auth 14],  VU [auth 1H],  VUA [auth 14],  VV [auth 1H],  VVA [auth 45],  VW [auth 1H],  VX [auth 1H],  VY [auth 1H],  VZ [auth 1H],  WAA [auth 1H],  WBA [auth 16],  WCA [auth 1G],  WD [auth 13],  WDA [auth 1G],  WE [auth 13],  WEA [auth 1G],  WF [auth 13],  WFA [auth 1G],  WG [auth 13],  WGA [auth 14],  WH [auth 13],  WHA [auth 14],  WIA [auth 14],  WJ [auth 1H],  WJA [auth 14],  WK [auth 1H],  WKA [auth 14],  WL [auth 1H],  WLA [auth 14],  WM [auth 1H],  WMA [auth 14],  WN [auth 1H],  WNA [auth 14],  WO [auth 1H],  WOA [auth 14],  WP [auth 1H],  WPA [auth 14],  WQ [auth 1H],  WQA [auth 14],  WR [auth 1H],  WRA [auth 14],  WS [auth 1H],  WSA [auth 14],  WT [auth 1H],  WTA [auth 14],  WU [auth 1H],  WUA [auth 14],  WV [auth 1H],  WVA [auth 85],  WW [auth 1H],  WX [auth 1H],  WY [auth 1H],  WZ [auth 1H],  XAA [auth 1H],  XBA [auth 16],  XCA [auth 1G],  XD [auth 13],  XDA [auth 1G],  XE [auth 13],  XEA [auth 1G],  XF [auth 13],  XFA [auth 1G],  XG [auth 13],  XGA [auth 14],  XH [auth 13],  XHA [auth 14],  XI [auth 5E],  XIA [auth 14],  XJ [auth 1H],  XJA [auth 14],  XK [auth 1H],  XKA [auth 14],  XL [auth 1H],  XLA [auth 14],  XM [auth 1H],  XMA [auth 14],  XN [auth 1H],  XNA [auth 14],  XO [auth 1H],  XOA [auth 14],  XP [auth 1H],  XPA [auth 14],  XQ [auth 1H],  XQA [auth 14],  XR [auth 1H],  XRA [auth 14],  XS [auth 1H],  XSA [auth 14],  XT [auth 1H],  XTA [auth 14],  XU [auth 1H],  XUA [auth 14],  XV [auth 1H],  XVA [auth C5],  XW [auth 1H],  XX [auth 1H],  XY [auth 1H],  XZ [auth 1H],  YAA [auth 1H],  YBA [auth 16],  YCA [auth 1G],  YD [auth 13],  YDA [auth 1G],  YE [auth 13],  YEA [auth 1G],  YF [auth 13],  YFA [auth 1G],  YG [auth 13],  YGA [auth 14],  YH [auth 13],  YHA [auth 14],  YI [auth 3I],  YIA [auth 14],  YJ [auth 1H],  YJA [auth 14],  YK [auth 1H],  YKA [auth 14],  YL [auth 1H],  YLA [auth 14],  YM [auth 1H],  YMA [auth 14],  YN [auth 1H],  YNA [auth 14],  YO [auth 1H],  YOA [auth 14],  YP [auth 1H],  YPA [auth 14],  YQ [auth 1H],  YQA [auth 14],  YR [auth 1H],  YRA [auth 14],  YS [auth 1H],  YSA [auth 14],  YT [auth 1H],  YTA [auth 14],  YU [auth 1H],  YUA [auth 14],  YV [auth 1H],  YW [auth 1H],  YX [auth 1H],  YY [auth 1H],  YZ [auth 1H],  ZAA [auth 1H],  ZBA [auth 16],  ZCA [auth 1G],  ZD [auth 13],  ZDA [auth 1G],  ZE [auth 13],  ZEA [auth 1G],  ZF [auth 13],  ZFA [auth 1G],  ZG [auth 13],  ZGA [auth 14],  ZH [auth 13],  ZHA [auth 14],  ZIA [auth 14],  ZJ [auth 1H],  ZJA [auth 14],  ZK [auth 1H],  ZKA [auth 14],  ZL [auth 1H],  ZLA [auth 14],  ZM [auth 1H],  ZMA [auth 14],  ZN [auth 1H],  ZNA [auth 14],  ZO [auth 1H],  ZOA [auth 14],  ZP [auth 1H],  ZPA [auth 14],  ZQ [auth 1H],  ZQA [auth 14],  ZR [auth 1H],  ZRA [auth 14],  ZS [auth 1H],  ZSA [auth 14],  ZT [auth 1H],  ZTA [auth 14],  ZU [auth 1H],  ZUA [auth 14],  ZV [auth 1H],  ZVA [auth L5],  ZW [auth 1H],  ZX [auth 1H],  ZY [auth 1H],  ZZ [auth 1H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.9α = 90
b = 450.9β = 90
c = 622.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 2.0: 2019-06-26
    Changes: Data collection, Non-polymer description, Structure summary