3TQ4

Crystal structure of M-PMV dUTPase with a mixed population of substrate (dUPNPP) and post-inversion product (dUMP) in the active sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE
A
152Mason-Pfizer monkey virusMutation(s): 1 
Gene Names: gag-pro
Find proteins for P07570 (Mason-Pfizer monkey virus)
Go to UniProtKB:  P07570
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.172 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 60.564α = 90.00
b = 60.564β = 90.00
c = 64.018γ = 120.00
Software Package:
Software NamePurpose
REFMACphasing
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description
  • Version 1.2: 2018-01-24
    Type: Database references