6YVN | pdb_00006yvn

Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 2.84 MGy exposure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.162 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.133 (Depositor), 0.136 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

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

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uridine 5'-monophosphate synthase260Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11172
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OMP
(Subject of Investigation/LOI)

Query on OMP


Download:Ideal Coordinates CCD File
B [auth A]OROTIDINE-5'-MONOPHOSPHATE
C10 H13 N2 O11 P
KYOBSHFOBAOFBF-XVFCMESISA-N
U5P

Query on U5P


Download:Ideal Coordinates CCD File
C [auth A]URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
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

Query on GOL


Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.162 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.133 (Depositor), 0.136 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.36α = 90
b = 116.88β = 90
c = 61.99γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    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: 2024-10-23
    Changes: Structure summary
  • Version 2.0: 2025-12-17
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description