4HKP

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N3-oxide

Structural Biology Knowledgebase: 4HKP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.161

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HKP

Classification: LYASE / LYASE INHIBITOR

Total Structure Weight: 69678.96

Macromolecule Entities
Molecule Chains Length Organism Details
Uridine 5'-monophosphate synthase A, B 312 Homo sapiens EC#: 4.1.1.23 IUBMB
Fragment: UNP residues 190-480
Gene Name(s): UMPS Gene View OK/SW-cl.21
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 5-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O9 P
QONOHPMEMVHOPP-UAKXSSHOSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
16B
Query on 16B

A N-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O9 P
DYOUVDKCXLKHKY-XVFCMESISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
16B N/A in BindingDB
N/A in BindingMoad
Ki: 28300 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.161
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.29 α = 90.00
b = 61.78 β = 112.90
c = 70.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-15
  • Released Date: 2012-11-14
  • Deposition author(s): To, T.K., Kotra, L.P., Pai, E.F.

Revision History

  • 2012-12-19
    Type: Citation | Details: Citation update