Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase.

Baker, P.J.Sawa, Y.Shibata, H.Sedelnikova, S.E.Rice, D.W.

(1998) Nat Struct Biol 5: 561-567

  • DOI: https://doi.org/10.1038/817
  • Primary Citation of Related Structures:  
    1PJB, 1PJC, 1SAY

  • PubMed Abstract: 

    The structure of the hexameric L-alanine dehydrogenase from Phormidium lapideum reveals that the subunit is constructed from two domains, each having the common dinucleotide binding fold. Despite there being no sequence similarity, the fold of alanine dehydrogenase is closely related to that of the family of D-2-hydroxyacid dehydrogenases, with a similar location of the active site, suggesting that these enzymes are related by divergent evolution. L-alanine dehydrogenase and the 2-hydroxyacid dehydrogenases also use equivalent functional groups to promote substrate recognition and catalysis. However, they are arranged differently on the enzyme surface, which has the effect of directing opposite faces of the keto acid to the dinucleotide in each case, forcing a change in absolute configuration of the product.

  • Organizational Affiliation

    The Krebs Institute, The Department of Molecular Biology & Biotechnology, The University of Sheffield, UK. P.baker@sheffield.ac.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-ALANINE DEHYDROGENASE361Phormidium lapideumMutation(s): 0 
Gene Names: ALADH
Find proteins for O52942 (Phormidium lapideum)
Explore O52942 
Go to UniProtKB:  O52942
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO52942
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.190 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.1α = 90
b = 123.1β = 90
c = 184.86γ = 120
Software Package:
Software NamePurpose
CCP4model building
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Other, Refinement description