3DBP

Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Complexed with 6-NH2-UMP

• PDB DOI: https://doi.org/10.2210/pdb3DBP/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-02 Released: 2009-06-23 
• Deposition Author(s): Liu, Y., To, T., Bello, A.M., Kotra, L.P., Pai, E.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.189 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Complexed with 6-NH2-UMP

Liu, Y., To, T., Bello, A.M., Kotra, L.P., Pai, E.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.81 kDa 
• Atom Count: 4,737 
• Modelled Residue Count: 514 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Orotidine 5'-phosphate decarboxylase	A, B	279	Homo sapiens	Mutation(s): 0  Gene Names: UMPS, OK/SW-cl.21 EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11172 (Homo sapiens) Explore P11172  Go to UniProtKB:  P11172
PHAROS:  P11172 GTEx:  ENSG00000114491

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUP	D [auth A], F [auth B]	6-AMINOURIDINE 5'-MONOPHOSPHATE C9 H14 N3 O9 P DUFXRFNPGXQQOI-YXZULKJRSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.189 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.118	α = 90
b = 61.558	β = 112.76
c = 70.565	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Adxv	data processing
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Liu, Y., To, T., Bello, A.M., Kotra, L.P., Pai, E.F.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description