1KM3

crystal structure of ODCase mutant K42A complexed with 6-azaUMP

Structural Biology Knowledgebase: 1KM3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.162

Literature

Macromolecules
Sequence Display for 1KM3

Classification: LYASE

Total Structure Weight: 27063.06

Macromolecule Entities
Molecule Chains Length Organism Details
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE A 247 Methanothermobacter thermautotrophicus EC#: 4.1.1.23 IUBMB
Mutation: K42A, R101P
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 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 (98) BindingDB

N/A in BindingMoad
Ki: 12400 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.162
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 58.35 α = 90.00
b = 103.18 β = 90.00
c = 73.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-13
  • Released Date: 2002-06-28
  • Deposition author(s): Wu, N., Gillon, W., Pai, E.F.

Revision History

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