1P3D

Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA and ANP.

Structural Biology Knowledgebase: 1P3D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 1P3D

Classification: LIGASE

Total Structure Weight: 108255.59

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-N-acetylmuramate--alanine ligase A, B 475 Haemophilus influenzae EC#: 6.3.2.8 IUBMB
Mutation: M1M, M15M, M31M, M110M, M115M, M135M, M138M, M187M, M194M, M199M, M209M, M228M, M236M, M371M, M400M
Gene Name(s): murC HI_1139
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L- ALANINE
C23 H36 N4 O20 P2
NTMMCWJNQNKACG-KBKUWGQMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ANP
Query on ANP

A, B PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.194
  • R-Value Work: 0.168
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 74.92 α = 90.00
b = 87.33 β = 104.86
c = 86.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-17
  • Released Date: 2003-07-15
  • Deposition author(s): Mol, C.D., Brooun, A., Dougan, D.R., Hilgers, M.T., Tari, L.W., Wijnands, R.A., Knuth, M.W., McRee, D.E., Swanson, R.V.

Revision History

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