› 5ofm

X-ray diffraction
1.5Å resolution

Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole

Released:
DOI: 10.2210/pdb5ofm/pdb
PDB entry 5ofm coloured by chain, front view.
PDB entry 5ofm coloured by chain, side view.
PDB entry 5ofm coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Unterlass JE, Basle A, Blackburn TJ, Tucker J, Cano C, Noble MEM, Curtin NJ

Function and Biology Details

Reactions catalysed: 
(S)-malate + NAD(+) = oxaloacetate + NADH
(R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH
3-phospho-D-glycerate + NAD(+) = 3-phosphonooxypyruvate + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128865 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-3-phosphoglycerate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 223 amino acids
Theoretical weight: 23.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43175 (Residues: 93-315; Coverage: 42%)
Gene names: PGDH3, PHGDH
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:
Ligand 9TT 2 x 9TT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P1
Unit cell:
a: 43.342Å b: 45.86Å c: 56.175Å
α: 97.91° β: 110.74° γ: 106.39°
R-values:
R R work R free
0.194 0.191 0.249
Expression system: Escherichia coli

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