2P1F

Human UMP Synthase (C-terminal Domain-Orotidine 5'-Monophosphate Decarboxylase)

• PDB DOI: https://doi.org/10.2210/pdb2P1F/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-05 Released: 2007-04-03 
• Deposition Author(s): Liu, Y., Tang, H.L., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.171 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 

Starting Model: experimental

Literature

Human UMP Synthase (C-terminal Domain-Orotidine 5'-Monophosphate Decarboxylase)

Liu, Y., Tang, H.L., 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,PQS (software)

Macromolecule Content

• Total Structure Weight: 32.26 kDa 
• Atom Count: 2,537 
• Modelled Residue Count: 259 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A	291	Homo sapiens	Mutation(s): 1  Gene Names: UMPS EC: 2.4.2.10 (UniProt), 4.1.1.23 (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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.171 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.314	α = 90
b = 116.875	β = 90
c = 61.946	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-03 
Deposition Author(s): Liu, Y., Tang, H.L., Pai, E.F.

Revision History  

• Version 1.0: 2007-04-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description