Pig muscle 3-PHOSPHOGLYCERATE KINASE complexed with 3-PG and MgADP.

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


A 1.8 A resolution structure of pig muscle 3-phosphoglycerate kinase with bound MgADP and 3-phosphoglycerate in open conformation: new insight into the role of the nucleotide in domain closure.

Szilagyi, A.N.Ghosh, M.Garman, E.Vas, M.

(2001) J Mol Biol 306: 499-511

  • DOI: https://doi.org/10.1006/jmbi.2000.4294
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    3-phosphoglycerate kinase (PGK) is a typical kinase with two structural domains. The domains each bind one of the two substrates, 3-phosphoglycerate (3-PG) and MgATP. For the phospho-transfer reaction to take place the substrates must be brought closer by a hinge-bending domain closure. Open and closed structures of the enzyme with different relative domain positions have been determined from different species, but a comprehensive description of this conformational transition is yet to be attained. Crystals of pig muscle PGK in complex with MgADP and 3-phosphoglycerate were grown under the conditions which have previously resulted in crystals of the closed, catalytically competent conformation of Trypanosoma brucei PGK. The X-ray structure of the pig muscle ternary complex was determined at 1.8 A and the model was refined to R=20.8% and Rfree=24.1%. Contrary to expectation, however, it represents an essentially open conformation compared to that of T. brucei PGK. In addition, the beta-phosphate group of ADP is mobile in the new structure, in contrast to its well-defined position in T. brucei PGK. An extensive comparison of the ternary complexes from these remote species has been carried out in order to establish general differences between the two conformations and is reported here. A second pair of the open and closed structures was also compared. These analyses have made it possible to define several characteristic changes which accompany the structural transition, in addition to those identified previously: (1) the operation of a hinge at beta-strand L in the inter-domain region which greatly affects the relative domain positions; (2) the rearrangement and movement of helix 8, regulated through the interactions with the nucleotide phosphate; and (3) the existence of another hinge between helix 14 and the rest of the C-terminal part of the chain, which allows fine adjustment of the N-domain position. The main hinge at beta-strand L acts in concert with the C-terminal hinge at helix 7 described previously. Simultaneous interactions of the nucleotide phosphate groups with the loop that precedes helix 8, beta-strand J and the N terminus of helix 13 are required for propagation of the nucleotide effect towards the beta-strand L molecular hinge. A detailed description of the role of nucleotide binding in the hinge operation is presented.

  • Organizational Affiliation

    Institute of Enzymology Biological Research Center, Hungarian Academy of Sciences, Budapest, H-1518, Hungary.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOGLYCERATE KINASE413Sus scrofaMutation(s): 0 
Find proteins for Q7SIB7 (Sus scrofa)
Explore Q7SIB7 
Go to UniProtKB:  Q7SIB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SIB7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AMP

Download Ideal Coordinates CCD File 
C10 H14 N5 O7 P
Query on 3PG

Download Ideal Coordinates CCD File 
C3 H7 O7 P
Query on MG

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
3PG BindingDB:  1HDI Kd: 1.09e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.5α = 90
b = 105.2β = 98.4
c = 35.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-13
    Changes: Data collection, Database references, Experimental preparation, Other
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description