1LOL

Crystal structure of orotidine monophosphate decarboxylase complex with XMP

Structural Biology Knowledgebase: 1LOL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 1LOL

Classification: LYASE

Total Structure Weight: 50900.61

Macromolecule Entities
Molecule Chains Length Organism Details
orotidine 5'-monophosphate decarboxylase A, B 229 Methanothermobacter thermautotrophicus EC#: 4.1.1.23 IUBMB
Mutation: M1L, R101P, 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
XMP
Query on XMP

A, B XANTHOSINE-5'-MONOPHOSPHATE
5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE (Synonym)
C10 H14 N4 O9 P
DCTLYFZHFGENCW-UUOKFMHZSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BU2
Query on BU2

A, B 1,3-BUTANEDIOL
C4 H10 O2
PUPZLCDOIYMWBV-BYPYZUCNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
XMP N/A in BindingDB
Ki: 410 nM  BindingMOAD
Ki: 410 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.193
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.57 α = 90.00
b = 55.48 β = 94.28
c = 66.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-06
  • Released Date: 2002-08-07
  • Deposition author(s): Wu, N., Pai, E.F.

Revision History

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