1X1Z

Orotidine 5'-monophosphate decarboxylase (odcase) complexed with BMP (produced from 6-cyanoump)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.162

Literature

Macromolecules
Sequence Display for 1X1Z

Classification: LYASE

Total Structure Weight: 55807.54

Macromolecule Entities
Molecule Chains Length Organism Details
Orotidine 5'-phosphate decarboxylase A, B 252 Methanothermobacter thermautotrophicus EC#: 4.1.1.23 IUBMB
Fragment: residues 1-225
Mutation: R101P, L226R, N227I
Gene Name(s): pyrF MTH_129
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 6-HYDROXYURIDINE-5'-PHOSPHATE
C9 H13 N2 O10 P
UDOBICLZEKUKCV-YXZULKJRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BMP N/A in BindingDB
Ki: 0.0088 nM  BindingMOAD
Ki: 0.0088 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.162
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 58.10 α = 90.00
b = 73.57 β = 119.28
c = 59.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-04-15
  • Released Date: 2005-12-06
  • Deposition author(s): Fujihashi, M., Bello, A.M., Poduch, E., Wei, L., Annedi, S.C., Pai, E.F., Kotra, L.P.

Revision History

  • 2008-04-30
    Type: Version format compliance
  • 2011-07-13
    Type: Non-polymer description, Version format compliance