7CMS

Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the specific interaction between Geobacillus stearothermophilus tryptophanyl-tRNA synthetase and antimicrobial Chuangxinmycin.

Fan, S.Lv, G.Feng, X.Wu, G.Jin, Y.Yan, M.Yang, Z.

(2022) J Biol Chem 298: 101580


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan--tRNA ligaseA, B328Geobacillus stearothermophilusMutation(s): 1 
Gene Names: trpS
EC: 6.1.1.2
UniProt
Find proteins for P00953 (Geobacillus stearothermophilus)
Explore P00953 
Go to UniProtKB:  P00953
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00953
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9E0 (Subject of Investigation/LOI)
Query on 9E0

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
(5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid
C12 H11 N O2 S
DKHFLDXCKWDVMF-UPONEAKYSA-N
 Ligand Interaction
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.675α = 90
b = 91.675β = 90
c = 152.37γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81761128016
National Natural Science Foundation of China (NSFC)China81621064
Ministry of Science and Technology (MoST, China)China2018YFA0901800

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references