2G76

Crystal structure of human 3-phosphoglycerate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Models: experimental
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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 NADClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human 3-phosphoglycerate dehydrogenase

Turnbull, A.P.Salah, E.Savitsky, P.Gileadi, O.von Delft, F.Edwards, A.Arrowsmith, C.Weigelt, J.Sundstrom, M.Oppermann, U.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-3-phosphoglycerate dehydrogenase
A, B
335Homo sapiensMutation(s): 0 
Gene Names: PHGDHPGDH3
EC: 1.1.1.95 (PDB Primary Data), 1.1.1.399 (UniProt), 1.1.1.37 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O43175 (Homo sapiens)
Explore O43175 
Go to UniProtKB:  O43175
PHAROS:  O43175
GTEx:  ENSG00000092621 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43175
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.084α = 90
b = 124.113β = 100.99
c = 59.502γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

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

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description