3GKR

Crystal Structure of Weissella viridescens FemX:UDP-MurNAc-hexapeptide complex

Structural Biology Knowledgebase: 3GKR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GKR

Classification: Transferase / Transferase Product

Total Structure Weight: 39732.42

Macromolecule Entities
Molecule Chains Length Organism Details
FemX A 336 Weissella viridescens EC#: 2.3.2.10 IUBMB
Gene Name(s): femX
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UDP-MurNAc-peptide B 5 Staphylococcus aureus

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

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ALA
Query on ALA

B ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
UMA
Query on UMA
B L-PEPTIDE LINKING C23 H36 N4 O20 P2 ALA
FGA
Query on FGA
B D-gamma-peptide, C-delta linking C5 H9 N O4 --
DAL
Query on DAL
B D-PEPTIDE LINKING C3 H7 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.173
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.32 α = 90.00
b = 101.84 β = 102.85
c = 46.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-11
  • Released Date: 2010-03-23
  • Deposition author(s): Delfosse, V., Piton, J., Villet, R., Lecerf, M., Arthur, M., Mayer, C.

Revision History

  • 2012-09-05
    Type: Biological assembly | Details: corrected biological assembly
  • 2012-08-01
    Type: Polymer description | Details: --
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Changed residue name in the sequence