3MW7 | pdb_00003mw7

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-UMP(produced from 5-fluoro-6-amino-UMP)

• PDB DOI: https://doi.org/10.2210/pdb3MW7/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-05 Released: 2011-04-06 
• Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-UMP(produced from 5-fluoro-6-amino-UMP)

Liu, Y., 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: 68.79 kDa 
• Atom Count: 4,017 
• Modeled Residue Count: 515 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A, B	312	Homo sapiens	Mutation(s): 0  Gene Names: gi|13960142, OK/SW-cl.21, UMPS 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5FU	C [auth A], D [auth B]	5-FLUORO-URIDINE-5'-MONOPHOSPHATE C9 H12 F N2 O9 P RNBMPPYRHNWTMA-UAKXSSHOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.29	α = 90
b = 61.742	β = 111.64
c = 71.212	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Liu, Y., Kotra, L.P., Pai, E.F.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description