SMTL ID : 9fdh.1

Closed Human phosphoglycerate kinase complex with BPG and ADP produced by cross-soaking a TSA crystal

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

monomer

Ligands

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

ADP.1: 28 residues within 4Å: Chain A: 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, G.341, V.342, F.343, E.344, G.372, G.373, G.374, D.375, T.376, G.396, G.397 Ligands: X15.2, PEG.3, MG.6 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.215, A:K.216, A:G.239, A:G.313, A:N.337, A:G.338, A:E.344, A:G.374, A:D.375, A:T.376, A:T.376 Water bridges: A:K.216 Salt bridges: A:K.216, A:K.220, A:K.220

1 x X15: 1,3-BISPHOSPHOGLYCERIC ACID(Non-covalent)

X15.2: 20 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, K.220, N.337, G.373, G.374, G.396, G.397 Ligands: ADP.1, MG.6 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:N.26, A:R.39, A:H.63, A:G.374, A:G.396, A:G.397 Water bridges: A:R.66, A:H.170, A:R.171, A:K.216, A:K.216, A:K.216, A:K.216, A:D.375, A:D.375, A:A.398 Salt bridges: A:R.39, A:R.39, A:H.63, A:R.66, A:R.123, A:R.171, A:K.216, A:K.216, A:K.216, A:K.220

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 6 residues within 4Å: Chain A: A.215, F.292, V.342, E.344, W.345 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.29 PEG.4: 7 residues within 4Å: Chain A: T.329, R.330, A.331, K.332, R.365, G.366, C.367 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.332 Water bridges: A:R.330

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: R.66, K.216, V.217, A.218, D.219 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: K.216, D.375 Ligands: ADP.1, X15.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.375, H2O.4, H2O.7

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

NA.7: 5 residues within 4Å: Chain A: D.24, R.39, A.42, L.189, T.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.24, A:D.24

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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