3TQ5

Crystal structure of M-PMV dUTPASE post-inversion product (dUMP) COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion

Barabas, O.Nemeth, V.Bodor, A.Perczel, A.Rosta, E.Kele, Z.Zagyva, I.Szabadka, Z.Grolmusz, V.I.Wilmanns, M.Vertessy, B.G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE152Mason-Pfizer monkey virusMutation(s): 1 
Gene Names: gag-pro
EC: 3.6.1.23
UniProt
Find proteins for P07570 (Mason-Pfizer monkey virus)
Explore P07570 
Go to UniProtKB:  P07570
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07570
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP

Download Ideal Coordinates CCD File 
B [auth A]2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.714α = 90
b = 60.714β = 90
c = 63.775γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
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: 2011-10-12
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description