6CAP

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report



Literature

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with Sisomicin

DeMirci, H.

To be published.

Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J
98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
K
116Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
L
124Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
M
118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
N
60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
O
87Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
P
83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
Q
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
R
70Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
S
80Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
B
234Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
T
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
U
24Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
C
206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
D
208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RIBOSOMAL PROTEIN S5
E
150Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
F
101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
G
155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
H
138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
I
127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 23
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')W15Thermus thermophilus HB8

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Entity ID: 1
MoleculeChainsLengthOrganism
16S Ribosomal RNA rRNAA1522Thermus thermophilus HB8
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 22
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')Y6Thermus thermophilus HB8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIS
Query on SIS

Download CCD File 
A
(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
C19 H37 N5 O7
URWAJWIAIPFPJE-YFMIWBNJSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, F, H, K, L, M, P, Q, S, T, W
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 400.97α = 90
b = 400.97β = 90
c = 175.05γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-01-31 
  • Released Date: 2018-07-25 
  • Deposition Author(s): DeMirci, H.

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release