Macromolecules
Sequence Display for 1DVJ

Classification: LYASE

Total Structure Weight: 107959.87

Macromolecule Entities
Molecule Chains Length Organism Details
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE A, B, C, D 246 Methanothermobacter thermautotrophicus EC#: 4.1.1.23 IUBMB
Mutation: R101P, N227I
Gene Name(s): pyrF MTH_129
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UP6
Query on UP6

A, B, C, D 6-AZA URIDINE 5'-MONOPHOSPHATE
6-AZA-UMP (Synonym)
C8 H12 N3 O9 P
LRVZOSYMNMNQFR-SHUUEZRQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UP6 Ki: 12400 nM (99) BindingDB

Ki: 510000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.174
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 72.95 α = 90.00
b = 98.62 β = 104.03
c = 73.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-03-30
  • Released Date: 2000-04-05
  • Deposition author(s): Wu, N., Mo, Y., Gao, J., Pai, E.F.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4