1DQX

CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)

Structural Biology Knowledgebase: 1DQX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 1DQX

Classification: LYASE

Total Structure Weight: 118751.86

Macromolecule Entities
Molecule Chains Length Organism Details
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE A, B, C, D 267 Saccharomyces cerevisiae EC#: 4.1.1.23 IUBMB
Mutation: S2H, N267D
Gene Name(s): URA3 YEL021W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 6-HYDROXYURIDINE-5'-PHOSPHATE
C9 H13 N2 O10 P
UDOBICLZEKUKCV-YXZULKJRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BMP Ki: 0.0088 - 0.009 nM (98) BindingDB

Ki: 0.009 nM  BindingMOAD
Ki: 0.009 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.213
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 79.89 α = 90.00
b = 79.97 β = 108.59
c = 98.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-01-05
  • Released Date: 2000-03-20
  • Deposition author(s): Milburn, M.V., Miller, B.G., Hassell, A.M., Wolfenden, R., Short, S.A.

Revision History

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