5JVG

The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.

Krupkin, M.Wekselman, I.Matzov, D.Eyal, Z.Diskin Posner, Y.Rozenberg, H.Zimmerman, E.Bashan, A.Yonath, A.

(2016) Proc Natl Acad Sci U S A 113: E6796-E6805

  • DOI: https://doi.org/10.1073/pnas.1614297113
  • Primary Citation of Related Structures:  
    5JVG, 5JVH

  • PubMed Abstract: 

    Two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against Enterococci, Staphylococci, and Streptococci, and other Gram-positive bacteria. Here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. Their extended binding sites span the A-tRNA entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the A-tRNA elbow, a mechanism not shared with other known antibiotics. Along with using the ribosomal components that bind and discriminate the A-tRNA-namely, ribosomal RNA (rRNA) helices H89, H91, and ribosomal proteins (rProtein) uL16-these structures revealed novel interactions with domain 2 of the CTC protein, a feature typical to various Gram-positive bacteria. Furthermore, analysis of these structures explained how single nucleotide mutations and methylations in helices H89 and H91 confer resistance to orthosomycins and revealed the sequence variations in 23S rRNA nucleotides alongside the difference in the lengths of the eukaryotic and prokaryotic α1 helix of protein uL16 that play a key role in the selectivity of those drugs. The accurate interpretation of the crystal structures that could be performed beyond that recently reported in cryo-EM models provide structural insights that may be useful for the design of novel pathogen-specific antibiotics, and for improving the potency of orthosomycins. Because both drugs are extensively metabolized in vivo, their environmental toxicity is very low, thus placing them at the frontline of drugs with reduced ecological hazards.


  • Organizational Affiliation

    Department of Structural Biology, Weizmann Institute, Rehovot 76100 001, Israel.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]275Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth B]211Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]205Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]180Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]185Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11H [auth F]144Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSS7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth G]174Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXY1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth H]134Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth I]156Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSK9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth J]141Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth K]116Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth L]114Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth M]166Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RWB4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth N]118Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth O]100Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth P]134Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth Q]95Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth R]115Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth S]237Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth T]91Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth U]81Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RRG8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth V]67Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth W]55Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3260Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth 1]55Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth 2]47Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth 3]66Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSW6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth X]2,877Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth Y]124Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6NO
Query on 6NO

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DA [auth X]Avilamycin
C61 H88 Cl2 O32
XIRGHRXBGGPPKY-GMJOKQQKSA-N
SPD
Query on SPD

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GQ [auth X],
HQ [auth X],
IQ [auth X]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
MPD
Query on MPD

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BQ [auth X],
CQ [auth X],
DQ [auth X],
EQ [auth X],
FQ [auth X]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG
Query on MG

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AB [auth X]
AC [auth X]
AD [auth X]
AE [auth X]
AF [auth X]
AB [auth X],
AC [auth X],
AD [auth X],
AE [auth X],
AF [auth X],
AG [auth X],
AH [auth X],
AI [auth X],
AJ [auth X],
AK [auth X],
AL [auth X],
AM [auth X],
AN [auth X],
AO [auth X],
AP [auth X],
AQ [auth X],
AR [auth Y],
BB [auth X],
BC [auth X],
BD [auth X],
BE [auth X],
BF [auth X],
BG [auth X],
BH [auth X],
BI [auth X],
BJ [auth X],
BK [auth X],
BL [auth X],
BM [auth X],
BN [auth X],
BO [auth X],
BP [auth X],
BR [auth Y],
CB [auth X],
CC [auth X],
CD [auth X],
CE [auth X],
CF [auth X],
CG [auth X],
CH [auth X],
CI [auth X],
CJ [auth X],
CK [auth X],
CL [auth X],
CM [auth X],
CN [auth X],
CO [auth X],
CP [auth X],
CR [auth Y],
DB [auth X],
DC [auth X],
DD [auth X],
DE [auth X],
DF [auth X],
DG [auth X],
DH [auth X],
DI [auth X],
DJ [auth X],
DK [auth X],
DL [auth X],
DM [auth X],
DN [auth X],
DO [auth X],
DP [auth X],
DR [auth Y],
EA [auth X],
EB [auth X],
EC [auth X],
ED [auth X],
EE [auth X],
EF [auth X],
EG [auth X],
EH [auth X],
EI [auth X],
EJ [auth X],
EK [auth X],
EL [auth X],
EM [auth X],
EN [auth X],
EO [auth X],
EP [auth X],
ER [auth Y],
FA [auth X],
FB [auth X],
FC [auth X],
FD [auth X],
FE [auth X],
FF [auth X],
FG [auth X],
FH [auth X],
FI [auth X],
FJ [auth X],
FK [auth X],
FL [auth X],
FM [auth X],
FN [auth X],
FO [auth X],
FP [auth X],
FR [auth Y],
GA [auth X],
GB [auth X],
GC [auth X],
GD [auth X],
GE [auth X],
GF [auth X],
GG [auth X],
GH [auth X],
GI [auth X],
GJ [auth X],
GK [auth X],
GL [auth X],
GM [auth X],
GN [auth X],
GO [auth X],
GP [auth X],
GR [auth Y],
HA [auth X],
HB [auth X],
HC [auth X],
HD [auth X],
HE [auth X],
HF [auth X],
HG [auth X],
HH [auth X],
HI [auth X],
HJ [auth X],
HK [auth X],
HL [auth X],
HM [auth X],
HN [auth X],
HO [auth X],
HP [auth X],
HR [auth Y],
IA [auth X],
IB [auth X],
IC [auth X],
ID [auth X],
IE [auth X],
IF [auth X],
IG [auth X],
IH [auth X],
II [auth X],
IJ [auth X],
IK [auth X],
IL [auth X],
IM [auth X],
IN [auth X],
IO [auth X],
IP [auth X],
IR [auth Y],
JA [auth X],
JB [auth X],
JC [auth X],
JD [auth X],
JE [auth X],
JF [auth X],
JG [auth X],
JH [auth X],
JI [auth X],
JJ [auth X],
JK [auth X],
JL [auth X],
JM [auth X],
JN [auth X],
JO [auth X],
JP [auth X],
JQ [auth X],
JR [auth A],
KA [auth X],
KB [auth X],
KC [auth X],
KD [auth X],
KE [auth X],
KF [auth X],
KG [auth X],
KH [auth X],
KI [auth X],
KJ [auth X],
KK [auth X],
KL [auth X],
KM [auth X],
KN [auth X],
KO [auth X],
KP [auth X],
KQ [auth X],
KR [auth J],
LA [auth X],
LB [auth X],
LC [auth X],
LD [auth X],
LE [auth X],
LF [auth X],
LG [auth X],
LH [auth X],
LI [auth X],
LJ [auth X],
LK [auth X],
LL [auth X],
LM [auth X],
LN [auth X],
LO [auth X],
LP [auth X],
LQ [auth X],
LR [auth K],
MA [auth X],
MB [auth X],
MC [auth X],
MD [auth X],
ME [auth X],
MF [auth X],
MG [auth X],
MH [auth X],
MI [auth X],
MJ [auth X],
MK [auth X],
ML [auth X],
MM [auth X],
MN [auth X],
MO [auth X],
MP [auth X],
MQ [auth X],
MR [auth M],
NA [auth X],
NB [auth X],
NC [auth X],
ND [auth X],
NE [auth X],
NF [auth X],
NG [auth X],
NH [auth X],
NI [auth X],
NJ [auth X],
NK [auth X],
NL [auth X],
NM [auth X],
NN [auth X],
NO [auth X],
NP [auth X],
NQ [auth X],
NR [auth N],
OA [auth X],
OB [auth X],
OC [auth X],
OD [auth X],
OE [auth X],
OF [auth X],
OG [auth X],
OH [auth X],
OI [auth X],
OJ [auth X],
OK [auth X],
OL [auth X],
OM [auth X],
ON [auth X],
OO [auth X],
OP [auth X],
OQ [auth X],
OR [auth T],
PA [auth X],
PB [auth X],
PC [auth X],
PD [auth X],
PE [auth X],
PF [auth X],
PG [auth X],
PH [auth X],
PI [auth X],
PJ [auth X],
PK [auth X],
PL [auth X],
PM [auth X],
PN [auth X],
PO [auth X],
PP [auth X],
PQ [auth X],
PR [auth 3],
QA [auth X],
QB [auth X],
QC [auth X],
QD [auth X],
QE [auth X],
QF [auth X],
QG [auth X],
QH [auth X],
QI [auth X],
QJ [auth X],
QK [auth X],
QL [auth X],
QM [auth X],
QN [auth X],
QO [auth X],
QP [auth X],
QQ [auth Y],
RA [auth X],
RB [auth X],
RC [auth X],
RD [auth X],
RE [auth X],
RF [auth X],
RG [auth X],
RH [auth X],
RI [auth X],
RJ [auth X],
RK [auth X],
RL [auth X],
RM [auth X],
RN [auth X],
RO [auth X],
RP [auth X],
RQ [auth Y],
SA [auth X],
SB [auth X],
SC [auth X],
SD [auth X],
SE [auth X],
SF [auth X],
SG [auth X],
SH [auth X],
SI [auth X],
SJ [auth X],
SK [auth X],
SL [auth X],
SM [auth X],
SN [auth X],
SO [auth X],
SP [auth X],
SQ [auth Y],
TA [auth X],
TB [auth X],
TC [auth X],
TD [auth X],
TE [auth X],
TF [auth X],
TG [auth X],
TH [auth X],
TI [auth X],
TJ [auth X],
TK [auth X],
TL [auth X],
TM [auth X],
TN [auth X],
TO [auth X],
TP [auth X],
TQ [auth Y],
UA [auth X],
UB [auth X],
UC [auth X],
UD [auth X],
UE [auth X],
UF [auth X],
UG [auth X],
UH [auth X],
UI [auth X],
UJ [auth X],
UK [auth X],
UL [auth X],
UM [auth X],
UN [auth X],
UO [auth X],
UP [auth X],
UQ [auth Y],
VA [auth X],
VB [auth X],
VC [auth X],
VD [auth X],
VE [auth X],
VF [auth X],
VG [auth X],
VH [auth X],
VI [auth X],
VJ [auth X],
VK [auth X],
VL [auth X],
VM [auth X],
VN [auth X],
VO [auth X],
VP [auth X],
VQ [auth Y],
WA [auth X],
WB [auth X],
WC [auth X],
WD [auth X],
WE [auth X],
WF [auth X],
WG [auth X],
WH [auth X],
WI [auth X],
WJ [auth X],
WK [auth X],
WL [auth X],
WM [auth X],
WN [auth X],
WO [auth X],
WP [auth X],
WQ [auth Y],
XA [auth X],
XB [auth X],
XC [auth X],
XD [auth X],
XE [auth X],
XF [auth X],
XG [auth X],
XH [auth X],
XI [auth X],
XJ [auth X],
XK [auth X],
XL [auth X],
XM [auth X],
XN [auth X],
XO [auth X],
XP [auth X],
XQ [auth Y],
YA [auth X],
YB [auth X],
YC [auth X],
YD [auth X],
YE [auth X],
YF [auth X],
YG [auth X],
YH [auth X],
YI [auth X],
YJ [auth X],
YK [auth X],
YL [auth X],
YM [auth X],
YN [auth X],
YO [auth X],
YP [auth X],
YQ [auth Y],
ZA [auth X],
ZB [auth X],
ZC [auth X],
ZD [auth X],
ZE [auth X],
ZF [auth X],
ZG [auth X],
ZH [auth X],
ZI [auth X],
ZJ [auth X],
ZK [auth X],
ZL [auth X],
ZM [auth X],
ZN [auth X],
ZO [auth X],
ZP [auth X],
ZQ [auth Y]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.43 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.034α = 90
b = 412.632β = 90
c = 698.142γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Structure summary
  • Version 1.2: 2019-09-25
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description