3PGK

The structure of yeast phosphoglycerate kinase at 0.25 nm resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 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


  • 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 compatibl ...

    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: 
    • 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
    • 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
    • Structure of Yeast Phosphoglycerate Kinase
      Bryant, T.N.,Watson, H.C.,Wendell, P.L.
      (1974) Nature 257: 14
    • 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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOGLYCERATE KINASE
A
416Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PGK1
EC: 2.7.2.3
Find proteins for P00560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: PGK1
Go to UniProtKB:  P00560
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
3PG
Query on 3PG

Download SDF File 
Download CCD File 
A
3-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
OSJPPGNTCRNQQC-UWTATZPHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.600α = 90.00
b = 54.400β = 134.40
c = 93.000γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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