3PGK | pdb_00003pgk

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 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.

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 
• Modeled 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
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Structure summary