4B6C

Structure of the M. smegmatis GyrB ATPase domain in complex with an aminopyrazinamide

Structural Biology Knowledgebase: 4B6C SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4B6C

Classification: ISOMERASE

Total Structure Weight: 44983.01

Macromolecule Entities
Molecule Chains Length Organism Details
DNA GYRASE SUBUNIT B A, B 196 Mycobacterium smegmatis EC#: 5.99.1.3 IUBMB
Fragment: ATPASE DOMAIN, RESIDUES 9-102,123-213,246-255
Mutation: V213D, V246G
Gene Name(s): gyrB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B5U
Query on B5U

A, B 6-(3,4-dimethylphenyl)-3-[[4-[3-(4-methylpiperazin- 1-yl)propoxy]phenyl]amino]pyrazine-2-carboxamide
C27 H34 N6 O2
SMJHCUSNBTWDKM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
B5U N/A in BindingDB
IC50: 690 nM  BindingMOAD
IC50: 690 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.199
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 43.46 α = 90.00
b = 82.25 β = 90.00
c = 191.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-09
  • Released Date: 2013-01-23
  • Deposition author(s): Tucker, J.A., Shirude, P.S., Madhavapeddi, P., Hussein, S., Basu, R., Ghorpade, S.

Revision History

  • 2013-04-03
    Type: Citation | Details: JRNL
  • 2013-04-03
    Type: Polymer description | Details: COMPND