SMTL ID : 5mxm.1

The X-ray structure of human M190I phosphoglycerate kinase 1 mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.374 Ligands: ADP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.374, H2O.5, H2O.6, H2O.7

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

3PG.2: 10 residues within 4Å: Chain A: D.23, N.25, R.38, H.62, R.65, R.122, G.166, T.167, R.170, K.215 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:D.23, A:N.25, A:R.38, A:R.38 Water bridges: A:R.65, A:R.122, A:R.122, A:K.215, A:K.215, A:K.215, A:G.373, A:G.373, A:G.395, A:G.396 Salt bridges: A:R.38, A:H.62, A:R.65, A:R.122, A:R.170, A:K.215, A:K.215

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

ADP.3: 21 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, N.336, P.338, G.340, V.341, E.343, G.371, G.372, G.373, D.374, T.375 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.214, A:K.215, A:G.238, A:G.312, A:N.336, A:E.343, A:G.373, A:D.374, A:T.375 Water bridges: A:D.374, A:D.374, A:G.396, A:G.396 Salt bridges: A:K.219, A:K.219

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 5 residues within 4Å: Chain A: H.169, R.170, Q.221, E.400, K.405 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.170, A:E.400, A:K.405 Water bridges: A:E.400 Salt bridges: A:E.400

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

2018-02-14

Peptides

Phosphoglycerate kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglycerate kinase 1

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