5BOD | pdb_00005bod

Crystal structure of Streptococcus pneumonia ParE inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5BOD/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-27 Released: 2015-06-17 
• Deposition Author(s): Tan, Y.W., Chen, G., Hung, A.W., Hill, J.
• Funding Organization(s): Agency for Science, Technology and Research (A*STAR) Joint Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.206 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Application of Fragment-based Drug Discovery against DNA GyraseB

Chen, G.Y., Ng, F.M., Tan, Y.W., Poulsen, A., Seetoh, W., Lin, G., Kang, C., Then, S.W., Ahmad, N.H., Wong, Y.L., Ng, H.Q., Chia, B.C.S., Lau, Q.Y., Hill, J., Hung, A.W., Keller, T.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.9 kDa 
• Atom Count: 1,558 
• Modeled Residue Count: 192 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	A	226	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: parE, spr0756 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q8DQB5 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DQB5  Go to UniProtKB:  Q8DQB5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTJ	B [auth A]	(2R)-N-[3-(3,5-dimethylphenyl)-1H-pyrazol-5-yl]-1,4-dioxane-2-carboxamide C16 H19 N3 O3 IFBWFTQSSMRHQI-CQSZACIVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.206 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.402	α = 90
b = 94.458	β = 90
c = 60.967	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
PHASER	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Tan, Y.W., Chen, G., Hung, A.W., Hill, J.

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Funding Organization	Location	Grant Number
Agency for Science, Technology and Research (A*STAR) Joint Council	Singapore	1231B105

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy