3BGJ | pdb_00003bgj

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP

• PDB DOI: https://doi.org/10.2210/pdb3BGJ/pdb

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


• Deposited: 2007-11-26 Released: 2008-11-18 
• Deposition Author(s): Liu, Y., Tang, H.L., Bello, A.M., Devalla, S., Kotra, L.P., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 6-iodo-UMP

Liu, Y., Tang, H.L., Bello, A.M., Devalla, S., 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: 64.24 kDa 
• Atom Count: 4,347 
• Modeled Residue Count: 514 
• Deposited Residue Count: 582 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A, B	291	Homo sapiens	Mutation(s): 0  Gene Names: 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	C [auth A], D [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.803	α = 90
b = 61.821	β = 111.66
c = 70.881	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Liu, Y., Tang, H.L., Bello, A.M., Devalla, S., Kotra, L.P., Pai, E.F.

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary