3PGK

The structure of yeast phosphoglycerate kinase at 0.25 nm resolution

• PDB DOI:  https://doi.org/10.2210/pdb3PGK/pdb
• Entry: 3PGK supersedes: 1PGK

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1982-07-15 Released: 1982-09-24 
• Deposition Author(s): Shaw, P.J., Walker, N.P., Watson, H.C.

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Experimental Data Snapshot

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

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: 6765200 
• DOI: https://doi.org/10.1002/j.1460-2075.1982.tb01366.x
• 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. A carboxyl-imidazole interaction appears to be involved in controlling the transition between the open and closed forms of the enzyme.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.37 kDa 
• Atom Count: 3,191 
• Modelled Residue Count: 416 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOGLYCERATE KINASE	A	416	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.7.2.3
UniProt
Find proteins for P00560 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00560  Go to UniProtKB:  P00560

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
3PG	D [auth A]	3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 126.6	α = 90
b = 54.4	β = 134.4
c = 93	γ = 90

Structure Validation

Entry History 

Deposition Data

• Released Date: 1982-09-24 
Deposition Author(s): Shaw, P.J., Walker, N.P., Watson, H.C.
• This entry supersedes: 1PGK

Revision History  

• 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