4DF1

Crystal structure of orotidine 5'-monophosphate decarboxylase from Thermoproteus neutrophilus complexed with inhibitor BMP

Structural Biology Knowledgebase: 4DF1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.150

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DF1

Classification: LYASE / LYASE inhibitor

Total Structure Weight: 44703.17

Macromolecule Entities
Molecule Chains Length Organism Details
Orotidine 5'-phosphate decarboxylase A, B 202 Pyrobaculum neutrophilum Gene Name(s): Tneu_0023

Small Molecules
Ligands 2 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)
NI
Query on NI

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.150
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.16 α = 90.00
b = 62.07 β = 97.46
c = 72.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-22
  • Released Date: 2013-01-23
  • Deposition author(s): Fedorov, A.A., Fedorov, E.V., Desai, B., Gerlt, J.A., Almo, S.C.

Revision History

No revisions since initial release