1PNV

Crystal Structure of TDP-epi-Vancosaminyltransferase GtfA in complexes with TDP and Vancomycin

Structural Biology Knowledgebase: 1PNV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 1PNV

Classification: TRANSFERASE / ANTIBIOTIC

Total Structure Weight: 87423.28

Macromolecule Entities
Molecule Chains Length Organism Details
GLYCOSYLTRANSFERASE GTFA A, B 404 Amycolatopsis orientalis EC#: 2.4.1.311 IUBMB
Gene Name(s): gtfA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
VANCOMYCIN C 7 Amycolatopsis orientalis

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

A THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

C BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RER
Query on RER

C (1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl- alpha-L-arabino-hexopyranose
VANCOSAMINE (Synonym)
C7 H15 N O3
OIJZDPGKNVKVBL-WNJXEPBRSA-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: 0.269
  • R-Value Work: 0.221
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 153.17 α = 90.00
b = 153.17 β = 90.00
c = 100.64 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-13
  • Released Date: 2003-08-12
  • Deposition author(s): Mulichak, A.M., Losey, H.C., Lu, W., Wawrzak, Z., Walsh, C.T., Garavito, R.M.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-27
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-27
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-27
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-27
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-27
    Type: Linkage | Details: Linkage
  • 2011-07-27
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-27
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4