2FVV

Human Diphosphoinositol polyphosphate phosphohydrolase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.222 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IHPClick on this verticalbar to view details

This is version 2.2 of the entry. See complete history


Literature

Crystal structure of human diphosphoinositol phosphatase 1

Thorsell, A.G.Persson, C.Graslund, S.Hammarstrom, M.Busam, R.D.Hallberg, B.M.

(2009) Proteins 77: 242-246


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diphosphoinositol polyphosphate phosphohydrolase 1194Homo sapiensMutation(s): 0 
Gene Names: NUDT3DIPPDIPP1
EC: 3.6.1.52 (PDB Primary Data), 3.6.1 (PDB Primary Data), 3.6.1.62 (UniProt), 3.6.1.61 (UniProt), 3.6.1.59 (UniProt), 3.6.1.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95989 (Homo sapiens)
Explore O95989 
Go to UniProtKB:  O95989
PHAROS:  O95989
GTEx:  ENSG00000272325 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95989
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.222 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.653α = 90
b = 59.9β = 90
c = 61.735γ = 90
Software Package:
Software NamePurpose
SHELXrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
SAINTdata reduction
XDSdata reduction
SADABSdata scaling
XSCALEdata scaling
SHELXDphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted IHPClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-11
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-23
    Changes: Data collection
  • Version 2.0: 2019-04-03
    Changes: Advisory, Atomic model, Data collection
  • Version 2.1: 2020-10-14
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2024-03-13
    Changes: Data collection, Database references