1P4N

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

Structural Biology Knowledgebase: 1P4N SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1P4N

Classification: Transferase / Transferase Substrate

Total Structure Weight: 39604.25

Macromolecule Entities
Molecule Chains Length Organism Details
FemX A 335 Weissella viridescens EC#: 2.3.2.10 IUBMB
Gene Name(s): femX
UDP-MurNAc-pentapeptide B 5 Staphylococcus aureus

Small Molecules
Ligands 2 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)
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: 1.9 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.172
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.20 α = 90.00
b = 100.61 β = 115.64
c = 46.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-23
  • Released Date: 2004-02-10
  • Deposition author(s): Biarrotte-Sorin, S., Maillard, A., Delettre, J., Sougakoff, W., Arthur, M., Mayer, C.

Revision History

  • 2012-08-01
    Type: Polymer description | Details: --
  • 2011-07-27
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-27
    Type: Linkage | Details: Linkage
  • 2011-07-27
    Type: Sequence database correspondence | Details: Changed residue name in the sequence
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4