SMTL ID : 2x13.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 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.11, H2O.11

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

3PG.2: 11 residues within 4Å: Chain A: D.23, N.25, R.38, H.62, R.65, R.122, G.166, T.167, H.169, R.170, K.215 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:D.23, A:N.25, A:R.38, A:R.38 Water bridges: A:R.122, A:R.122, A:G.166, A:H.169, A:R.170, A:K.215, A:K.215, A:K.215, A:G.373, A:G.373, A:G.395 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.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, G.395 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.214, A:G.238, A:G.312, A:N.336, A:E.343, A:G.372, A:G.373, A:D.374, A:D.374, A:T.375 Water bridges: A:K.219, A:K.219, A:G.395 Salt bridges: A:K.219, A:K.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pellegrini, E. et al., Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide. Structure (2024)

Release Date

2010-12-29

Peptides

PHOSPHOGLYCERATE KINASE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PHOSPHOGLYCERATE KINASE 1

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