1KHR

Crystal Structure of Vat(D) in Complex with Virginiamycin and Coenzyme A

Structural Biology Knowledgebase: 1KHR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 1KHR

Classification: transferase / antibiotic

Total Structure Weight: 148234.97

Macromolecule Entities
Molecule Chains Length Organism Details
STREPTOGRAMIN A ACETYLTRANSFERASE A, B, C..., D, E, FA, B, C, D, E, F 209 Enterococcus faecium EC#: 2.3.1 IUBMB
Gene Name(s): vatD satA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
VIR
Query on VIR

A, E VIRGINIAMYCIN M1
C28 H35 N3 O7
DAIKHDNSXMZDCU-FQTGFAPKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.186
  • Space Group: F 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 186.10 α = 90.00
b = 185.90 β = 90.00
c = 186.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-30
  • Released Date: 2002-02-20
  • Deposition author(s): Sugantino, M., Roderick, S.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4