6YVK

Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 0.71 MGy exposure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.2 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uridine 5'-monophosphate synthase260Homo sapiensMutation(s): 0 
Gene Names: UMPSOK/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
Expand
  • 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
U
Query on U

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: 0.155 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.29α = 90
b = 116.82β = 90
c = 61.95γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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