4DBE

Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus complexed with inhibitor BMP

Structural Biology Knowledgebase: 4DBE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DBE

Classification: LYASE / LYASE INHIBITOR

Total Structure Weight: 50520.91

Macromolecule Entities
Molecule Chains Length Organism Details
Orotidine 5'-phosphate decarboxylase A, B 222 Sulfolobus solfataricus EC#: 4.1.1.23 IUBMB
Gene Name(s): pyrF Ssol_1680

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

A, B 6-HYDROXYURIDINE-5'-PHOSPHATE
C9 H13 N2 O10 P
UDOBICLZEKUKCV-YXZULKJRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.195
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 72.41 α = 90.00
b = 41.54 β = 94.08
c = 73.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-14
  • Released Date: 2013-01-16
  • Deposition author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Revision History

No revisions since initial release