3TRN

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 1 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
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.566α = 90
b = 60.566β = 90
c = 63.524γ = 120
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

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: 2011-10-12
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection
  • Version 1.4: 2024-10-16
    Changes: Structure summary