› 4axx

X-ray diffraction
1.74Å resolution

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP 3-phosphoglycerate and beryllium trifluoride

Released:
DOI: 10.2210/pdb4axx/pdb
PDB entry 4axx coloured by chain, front view.
PDB entry 4axx coloured by chain, side view.
PDB entry 4axx coloured by chain, top view.
Source organism: Homo sapiens
Entry author: Bowler MW

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 Chain: A
Molecule details ›
Chain: A
Length: 417 amino acids
Theoretical weight: 44.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P00558 (Residues: 1-417; 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 1 x MG
Ligand CL 1 x CL
Ligand ADP 1 x ADP
Ligand 3PG 1 x 3PG
Ligand BEF 1 x BEF
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 38.82Å b: 90.8Å c: 108.54Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.17 0.206
Expression system: Escherichia coli BL21

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