SMTL ID : 5m6z.1

The X-ray structure of human M189I PGK-1 mutant in partially closed conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.1: 10 residues within 4Å: Chain A: D.23, N.25, R.38, H.62, R.65, R.122, G.166, T.167, R.170 Ligands: PO4.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.25, A:R.38, A:T.167 Salt bridges: A:R.38, A:H.62, A:H.62, A:R.65, A:R.122, A:R.170

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: G.394, G.395, G.396 Ligands: 3PG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.395, A:G.396 Water bridges: A:G.166

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 16 residues within 4Å: Chain A: G.213, A.214, K.215, K.219, G.237, G.238, F.241, L.256, G.312, L.313, G.340, V.341, E.343, D.374 Ligands: MG.4, MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.214, A:K.215, A:G.238, A:G.312, A:E.343, A:D.374, A:D.374 Water bridges: A:G.237, A:D.374, A:D.374 Salt bridges: A:K.219

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: G.212, G.213, K.219, G.337 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: A.214, K.215, D.218, K.219 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fiorillo, A. et al., The phosphoglycerate kinase 1 variants found in carcinoma cells display different catalytic activity and conformational stability compared to the native enzyme. PLoS ONE (2018)

Release Date

2017-11-29

Peptides

Phosphoglycerate kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglycerate kinase 1

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