› 2y3i

X-ray diffraction
2.9Å resolution

The structure of the fully closed conformation of human PGK in complex with L-ADP, 3PG and the TSA aluminium tetrafluoride

Released:
DOI: 10.2210/pdb2y3i/pdb
PDB entry 2y3i coloured by chain, front view.
PDB entry 2y3i coloured by chain, side view.
PDB entry 2y3i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Interaction of human 3-phosphoglycerate kinase with its two substrates: is substrate antagonism a kinetic advantage?
Lallemand P, Chaloin L, Roy B, Barman T, Bowler MW, Lionne C
J Mol Biol 409 742-57 (2011)
PMID: 21549713

Function and Biology Details

Reaction catalysed: 
ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132717 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphoglycerate kinase 1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 416 amino acids
Theoretical weight: 44.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P00558 (Residues: 1-416; Coverage: 100%)
Gene names: MIG10, OK/SW-cl.110, PGK1, PGKA
Sequence domains: Phosphoglycerate kinase
Structure domains: Phosphoglycerate kinase, N-terminal domain

Ligands and Environments

5 bound ligands:
Ligand MG 2 x MG
Ligand CL 2 x CL
Ligand LA8 2 x LA8
Ligand ALF 2 x ALF
Ligand 3PG 2 x 3PG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P212121
Unit cell:
a: 38.419Å b: 103.877Å c: 203.094Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.265 0.263 0.303
Expression system: Escherichia coli BL21

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Citations

1 review citation

Conformational dynamics in phosphoglycerate kinase, an open and shut case?
Bowler MW. (2013)
8 other articles