SMTL ID : 9fdn.1

Human phosphoglycerate kinase in complex with ATP and 3PG formed by cross-soaking a TSA crystal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: K.216, D.375 Ligands: ATP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.216 Water bridges: A:D.375, A:D.375

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 30 residues within 4Å: Chain A: R.39, G.214, A.215, K.216, K.220, G.238, G.239, F.242, L.257, F.292, G.313, L.314, N.337, G.338, P.339, V.340, G.341, V.342, F.343, E.344, G.372, G.373, G.374, D.375, T.376, G.396, G.397 Ligands: NA.1, 3PG.3, PG4.4 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:A.215, A:K.216, A:G.239, A:G.313, A:N.337, A:E.344, A:G.373, A:G.374, A:D.375, A:T.376, A:T.376, A:G.396, A:G.397 Water bridges: A:N.26, A:G.167, A:K.216, A:K.216, A:K.216, A:E.344, A:A.398 Salt bridges: A:R.39, A:K.216, A:K.216, A:K.220, A:K.220, A:K.220

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

3PG.3: 14 residues within 4Å: Chain A: D.24, N.26, R.39, H.63, R.66, R.123, G.167, T.168, H.170, R.171, H.173, K.216, G.397 Ligands: ATP.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:D.24, A:N.26, A:R.39, A:H.63, A:G.167 Water bridges: A:R.39, A:R.66, A:H.170, A:H.170, A:R.171, A:K.216, A:K.216, A:K.216 Salt bridges: A:R.39, A:H.63, A:R.66, A:R.123, A:R.171, A:K.216, A:K.216

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 9 residues within 4Å: Chain A: K.30, A.215, L.257, F.292, M.312, V.342, E.344, W.345 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cliff, M.J. et al., The role of magnesium in catalysis by phosphoglycerate kinase. To be published

Release Date

2025-05-28

Peptides

Phosphoglycerate kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phosphoglycerate kinase 1

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