7OTU

Human OMPD-domain of UMPS in complex with 6-hydroxy-UMP at 0.95 Angstroms resolution, crystal 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.097 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Isoform 2 of 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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.097 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.893α = 90
b = 116.724β = 90
c = 61.898γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-05-04
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description