SMTL ID : 5m3u.1

The X-ray structure of human V216F phosphoglycerate kinase 1 mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: G.213, A.214, K.219, G.237, G.238, F.241, L.256, G.312, L.313, N.336, G.337, P.338, G.340, V.341, E.343, G.372, G.373, D.374, T.375 Ligands: MG.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.214, A:G.238, A:G.312, A:E.343, A:G.373, A:D.374, A:D.374, A:T.375 Water bridges: A:K.215, A:G.237 Salt bridges: A:K.219, A:K.219

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

3PG.2: 9 residues within 4Å: Chain A: D.23, N.25, R.38, H.62, R.65, R.122, T.167, R.170 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.23, A:N.25, A:R.38 Water bridges: A:R.170, A:G.396 Salt bridges: A:R.38, A:H.62, A:R.65, A:R.122, A:R.170

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.374 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.374, H2O.1, H2O.5 MG.4: 4 residues within 4Å: Chain A: K.5, D.411, L.413, N.415 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.411, A:L.413, H2O.3 MG.5: 3 residues within 4Å: Chain A: G.395, G.396 Ligands: 3PG.2 No protein-ligand interaction detected (PLIP)

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

2017-12-20

Peptides

Phosphoglycerate kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglycerate kinase 1