9HY0 | pdb_00009hy0

Variant T321A of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP at 0.95 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb9HY0/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-01-09 Released: 2026-01-21 
• Deposition Author(s): Kirck, L.L., Tittmann, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.131 (Depositor), 0.131 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.123 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

Literature

Variant T321A of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the product UMP at 0.95 Angstrom resolution

Kirck, L.L., Tittmann, K.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.61 kDa 
• Atom Count: 2,600 
• Modeled Residue Count: 257 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A	258	Homo sapiens	Mutation(s): 1  Gene Names: UMPS, OK/SW-cl.21 EC: 2.4.2.10 (PDB Primary Data), 4.1.1.23 (PDB Primary Data)
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 (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
PRO	C [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.131 (Depositor), 0.131 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.123 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.06	α = 90
b = 117.22	β = 90
c = 60.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Kirck, L.L., Tittmann, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release