3PGK

The structure of yeast phosphoglycerate kinase at 0.25 nm resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Sequence and structure of yeast phosphoglycerate kinase.

Watson, H.C.Walker, N.P.Shaw, P.J.Bryant, T.N.Wendell, P.L.Fothergill, L.A.Perkins, R.E.Conroy, S.C.Dobson, M.J.Tuite, M.F.

(1982) EMBO J 1: 1635-1640

  • Primary Citation of Related Structures:  
    3PGK

  • PubMed Abstract: 
  • The structure of yeast phosphoglycerate kinase has been determined with data obtained from amino acid sequence, nucleotide sequence, and X-ray crystallographic studies. The substrate binding sites, as deduced from electron density maps, are compatible with known substrate specificity and the stereochemical requirements for the enzymic reaction ...

    The structure of yeast phosphoglycerate kinase has been determined with data obtained from amino acid sequence, nucleotide sequence, and X-ray crystallographic studies. The substrate binding sites, as deduced from electron density maps, are compatible with known substrate specificity and the stereochemical requirements for the enzymic reaction. A carboxyl-imidazole interaction appears to be involved in controlling the transition between the open and closed forms of the enzyme.


    Related Citations: 
    • The Complete Amino Acid Sequence of Yeast Phosphoglycerate Kinase
      Perkins, R.E., Conroy, S.C., Dunbar, B., Fothergill, L.A., Tuite, M.F., Dobson, M.J., Kingsman, S.M., Kingsman, A.J.
      (1983) Biochem J 211: 199
    • Sequence and Structure of Yeast Phosphoglycerate Kinase
      Watson, H.C., Walker, N.P.C., Shaw, P.J., Bryant, T.N., Wendell, P.L., Fothergill, L.A., Perkins, R.E., Conroy, S.C., Dobson, M.J., Tuite, M.F., Kingsman, A.J., Kingsman, S.M.
      (1982) EMBO J 1: 1635
    • Structure of Yeast Phosphoglycerate Kinase
      Bryant, T.N., Watson, H.C., Wendell, P.L.
      (1974) Nature 257: 14
    • Low Resolution Structure of Yeast Phosphoglycerate Kinase
      Wendell, P.L., Bryant, T.N., Watson, H.C.
      (1972) Nature New Biol 240: 134
    • Crystallographic Study of Yeast Phosphoglycerate Kinase
      Watson, H.C., Wendell, P.L., Scopes, R.K.
      (1971) J Mol Biol 57: 623

    Organizational Affiliation

    State Key Laboratory of Virology, College of Life Sciences, Medical Research Institute, Wuhan University, Wuhan, P. R. China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOGLYCERATE KINASEA416Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.2.3
UniProt
Find proteins for P00560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00560 
Go to UniProtKB:  P00560
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
3PG
Query on 3PG

Download Ideal Coordinates CCD File 
D [auth A]3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.6α = 90
b = 54.4β = 134.4
c = 93γ = 90

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1982-09-24
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other