1GPD

STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase.

Moras, D.Olsen, K.W.Sabesan, M.N.Buehner, M.Ford, G.C.Rossmann, M.G.

(1975) J Biol Chem 250: 9137-9162

  • DOI: https://doi.org/10.2210/pdb1gpd/pdb
  • Primary Citation of Related Structures:  
    1GPD

  • PubMed Abstract: 

    An improved electron density map of lobster holo-D-glyceraldehyde-3-phosphate dehydrogenase has been computed to 2.9 A resolution based on two heavy atom isomorphous derivatives. This has been averaged only over the Q molecular 2-fold axis, which is known to be exact in the human holoenzyme. The map showed possible asymmetry between the subunits in which the active centers are closely related across the R axis (that is, between the red and green or between the yellow and blue subunits). A difference map between the electron density of citrate and sulfate-soaked crystals gave further evidence for possible asymmetry. The major differences of electron density between R axis-related subunits appear around the active center and suggest the following interpretations. 1. The conformation of the adenine about the glycosidic bond is the more frequently observed anti with a C-2' endo conformation for the ribose ring in the red and yellow subunits, but is probably syn with a C-3' endo conformation in the green and blue subunits.2. The adenine ribose has its 3'-hydroxyl group hydrogen-bonded to a main chain carbonyl group in the red and yellow subunits but not in the green and blue subunits, as a consequence of the differing ribose conformations. 3. Cysteine-149 is more closely associated with histidine-176 in the green and blue subunits, and appears nearer the nicotinamide in the red and yellow subunits.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASEA [auth G],
B [auth R]
334Homarus americanusMutation(s): 0 
EC: 1.2.1.12
UniProt
Find proteins for P00357 (Homarus americanus)
Explore P00357 
Go to UniProtKB:  P00357
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00357
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149α = 90
b = 139.1β = 90
c = 80.7γ = 90

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1977-02-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2014-10-29
    Changes: Derived calculations
  • Version 2.0: 2023-09-27
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2024-10-30
    Changes: Structure summary