1AJ6

NOVOBIOCIN-RESISTANT MUTANT (R136H) OF THE N-TERMINAL 24 KDA FRAGMENT OF DNA GYRASE B COMPLEXED WITH NOVOBIOCIN AT 2.3 ANGSTROMS RESOLUTION

Structural Biology Knowledgebase: 1AJ6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 1AJ6

Classification: TOPOISOMERASE

Total Structure Weight: 24653.76

Macromolecule Entities
Molecule Chains Length Organism Details
GYRASE A 219 Escherichia coli EC#: 5.99.1.3 IUBMB
Fragment: N-TERMINAL 24 KDA
Mutation: R136H
Gene Name(s): gyrB acrB cou himB hisU nalC parA pcbA b3699 JW5625
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NOV
Query on NOV

A 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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NOV Ki: 14 nM (99) BindingDB
ΔG: -42.7 kJ/mol (99) BindingDB
ΔH: -51.8 kJ/mol (99) BindingDB
-TΔS: 9.1 kJ/mol (99) BindingDB

Kd: 1200 nM  BindingMOAD
Kd: 1200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.195
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 39.50 α = 90.00
b = 47.72 β = 90.00
c = 114.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1997-05-15
  • Released Date: 1998-05-20
  • Deposition author(s): Weston, S.A., Tunnicliffe, A., Pauptit, R.A.

Revision History

  • 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