1KIJ

Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin

Structural Biology Knowledgebase: 1KIJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 1KIJ

Classification: ISOMERASE

Total Structure Weight: 86761.10

Macromolecule Entities
Molecule Chains Length Organism Details
DNA GYRASE SUBUNIT B A, B 390 Thermus thermophilus EC#: 5.99.1.3 IUBMB
Fragment: 43K domain
Gene Name(s): gyrB TTHA1586
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NOVOBIOCIN
5-di- C-methyl-alpha-l-lyxofuranoside, (Synonym)
C31 H36 N2 O11
YJQPYGGHQPGBLI-KGSXXDOSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

A, B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.206
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 44.88 α = 90.00
b = 125.55 β = 96.36
c = 79.83 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-03
  • Released Date: 2002-06-03
  • Deposition author(s): Lamour, V., Hoermann, L., Jeltsch, J.-M., Oudet, P., Moras, D.

Revision History

  • 2016-06-01
    Type: Source and taxonomy | Details: --
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4