6YVO | pdb_00006yvo

Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 3.55 MGy exposure

• PDB DOI: https://doi.org/10.2210/pdb6YVO/pdb

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


• Deposited: 2020-04-28 Released: 2022-02-23 
• Deposition Author(s): Tittmann, K., Rindfleisch, S., Krull, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Starting Model: experimental

Literature

Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis

Rindfleisch, S., Krull, M., Uranga, J., Schmidt, T., Rabe von Pappenheim, F., Kirck, L.L., Balouri, A., Schneider, T., Chari, A., Kluger, R., Bourenkov, G., Diederichsen, U., Mata, R.A., Tittmann, K.

(2022) Nat Catal 5: 332-341

• DOI: https://doi.org/10.1038/s41929-022-00771-w

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: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 29.73 kDa 
• Atom Count: 2,810 
• Modelled Residue Count: 256 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A	260	Homo sapiens	Mutation(s): 0  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OMP (Subject of Investigation/LOI)	B [auth A]	OROTIDINE-5'-MONOPHOSPHATE C10 H13 N2 O11 P KYOBSHFOBAOFBF-XVFCMESISA-N
U	C [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.39	α = 90
b = 116.9	β = 90
c = 62	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Tittmann, K., Rindfleisch, S., Krull, M.

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary