SMTL ID : 7rcm.1

Crystal Structure of ADP-bound Galactokinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: T.77, S.79, A.82, W.106, Y.109, V.129, S.131, P.134, L.135, G.136, G.137, G.138, L.139, S.140, S.141, S.142, L.145 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:T.77, A:T.77, A:S.79, A:G.136, A:G.137, A:G.138, A:S.140, A:S.141, A:S.142, A:S.142 Water bridges: A:R.37, A:T.78, A:R.105, A:S.131, A:L.139, A:S.142, A:A.143, A:E.174 ADP.8: 19 residues within 4Å: Chain B: T.77, S.79, A.82, W.106, Y.109, V.129, S.131, P.134, L.135, G.136, G.137, G.138, L.139, S.140, S.141, S.142, L.145, R.228 Ligands: MG.13 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:S.79, B:G.136, B:G.137, B:G.138, B:S.140, B:S.141, B:S.142 Water bridges: B:R.37, B:T.61, B:T.77, B:S.79, B:Y.109, B:S.131, B:P.134, B:L.139, B:A.143, B:R.228 Salt bridges: B:R.228

2 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.2: 12 residues within 4Å: Chain A: R.37, E.43, H.44, D.46, Y.47, C.182, G.183, M.185, D.186, Y.236, G.345, G.346 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:H.44, A:D.46, A:G.183, A:G.183, A:D.186 Water bridges: A:R.37, A:T.45, A:D.186, A:D.186, A:Q.187, A:G.346 Salt bridges: A:R.37 GLA.9: 12 residues within 4Å: Chain B: R.37, E.43, H.44, D.46, Y.47, C.182, G.183, M.185, D.186, Y.236, G.345, G.346 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:H.44, B:D.46, B:G.183, B:G.183, B:D.186, B:Y.236, B:G.346 Water bridges: B:R.37, B:R.37, B:T.45, B:D.186, B:Q.187, B:Q.187 Salt bridges: B:R.37

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 2 residues within 4Å: Chain A: R.267, R.279 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.267, A:R.279 PO4.4: 3 residues within 4Å: Chain A: H.363, H.367, E.370 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.363, A:H.367 PO4.5: 2 residues within 4Å: Chain A: Q.172, H.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.172, A:Q.172 Salt bridges: A:H.175 PO4.10: 2 residues within 4Å: Chain B: H.363, H.367 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.363, B:H.367 PO4.11: 3 residues within 4Å: Chain B: R.267, R.276, R.279 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.267 Salt bridges: B:R.279 PO4.12: 2 residues within 4Å: Chain B: S.271, K.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.270, B:K.272

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: S.142 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.142, H2O.1, H2O.2, H2O.2 MG.13: 2 residues within 4Å: Chain B: S.142 Ligands: ADP.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.142, H2O.5, H2O.8

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

NA.7: 3 residues within 4Å: Chain A: Q.369, Y.372, G.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.374 NA.15: 3 residues within 4Å: Chain B: Q.369, Y.372, G.374 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.369, B:G.374

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain B: Y.47, Q.171, R.240 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.47, B:Q.171, B:R.240, B:R.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors. J.Med.Chem. (2021)

Release Date

2021-09-29

Peptides

Galactokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Galactokinase

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