SMTL ID : 4en4.1

Crystal Structure of the Ternary Human PL Kinase-Ginkgotoxin-MgATP Complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.118 Ligands: ATP.4, MPD.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.118, H2O.4, H2O.4 MG.3: 5 residues within 4Å: Chain A: V.115, D.235 Ligands: ATP.4, GT0.5, GT1.10 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.235 MG.11: 3 residues within 4Å: Chain B: D.118 Ligands: ATP.14, MPD.17 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.118, H2O.5, H2O.5 MG.13: 5 residues within 4Å: Chain B: V.115, D.235 Ligands: ATP.14, GT1.15, GT0.24 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.235

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

NA.2: 7 residues within 4Å: Chain A: D.113, T.148, P.149, N.150, E.153, T.186 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.113, A:T.186 NA.12: 7 residues within 4Å: Chain B: D.113, T.148, P.149, N.150, E.153, T.186 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.113, B:T.148

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

ATP.4: 23 residues within 4Å: Chain A: D.113, D.118, Y.127, N.150, E.153, T.186, S.187, V.201, R.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, L.263, L.267 Ligands: MG.1, NA.2, MG.3, MPD.6, GT1.10 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.150, A:E.153, A:T.186, A:T.186, A:S.187, A:V.226, A:V.226 Water bridges: A:E.153 ATP.14: 24 residues within 4Å: Chain B: D.113, V.115, D.118, N.150, E.153, T.186, S.187, L.199, V.201, R.224, K.225, V.226, A.228, F.230, T.233, G.234, F.237, L.263, L.267 Ligands: MG.11, NA.12, MG.13, GT1.15, MPD.17 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.150, B:T.186, B:T.186, B:S.187, B:V.226, B:V.226, B:T.233 Water bridges: B:T.148, B:E.153, B:F.230, B:T.233

2 x GT0: 5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol(Non-covalent)

GT0.5: 9 residues within 4Å: Chain A: S.12, G.20, H.46, T.47, Y.84, V.231, D.235 Ligands: MG.3, GT1.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.47 Hydrogen bonds: A:S.12, A:G.20, A:T.47, A:T.47, A:D.235 Water bridges: A:Y.84, A:Y.84 GT0.24: 10 residues within 4Å: Chain B: S.12, V.19, G.20, F.43, H.46, T.47, V.231, D.235 Ligands: MG.13, GT1.15 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.19, B:F.43 Hydrogen bonds: B:S.12, B:G.20, B:T.47, B:D.235 Water bridges: B:Y.84

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 5 residues within 4Å: Chain A: D.118, W.120, L.199 Ligands: MG.1, ATP.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.120, A:L.199 Water bridges: A:K.119 MPD.16: 6 residues within 4Å: Chain B: D.181, R.206, R.207, R.208, V.214 Ligands: MPD.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.214 Hydrogen bonds: B:D.181, B:R.206 MPD.17: 4 residues within 4Å: Chain B: D.118, W.120 Ligands: MG.11, ATP.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.120 Hydrogen bonds: B:D.118 Water bridges: B:S.187 MPD.18: 1 residues within 4Å: Chain B: L.312 No protein-ligand interaction detected (PLIP) MPD.19: 3 residues within 4Å: Chain B: Q.165, P.191, P.193 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.191, B:P.193 Water bridges: B:Q.165 MPD.20: 5 residues within 4Å: Chain B: A.144, D.145, G.179, D.181 Ligands: MPD.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.181 Water bridges: B:A.144

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: Q.63, R.70, M.93, E.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.70, A:R.70, A:E.100 SO4.8: 4 residues within 4Å: Chain A: E.155, G.159, R.160, K.161 No protein-ligand interaction detected (PLIP) SO4.9: 6 residues within 4Å: Chain A: C.5, L.31, G.32, F.33, H.246, K.247 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.34 SO4.21: 2 residues within 4Å: Chain B: E.155, G.159 No protein-ligand interaction detected (PLIP) SO4.22: 4 residues within 4Å: Chain B: Q.63, R.70, D.96, E.100 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.70 SO4.23: 4 residues within 4Å: Chain B: L.31, G.32, F.33, K.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.5 Salt bridges: B:K.247

2 x GT1: [5-hydroxy-4-(methoxymethyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

GT1.10: 12 residues within 4Å: Chain A: S.12, G.20, T.47, Y.84, V.231, G.232, T.233, G.234, D.235 Ligands: MG.3, ATP.4, GT0.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.84, A:V.231 Hydrogen bonds: A:G.20, A:T.47, A:G.232, A:T.233, A:G.234, A:D.235 Water bridges: A:Y.84, A:Y.84, A:Y.127, A:Y.127 GT1.15: 13 residues within 4Å: Chain B: S.12, V.19, G.20, T.47, Y.84, V.231, G.232, T.233, G.234, D.235 Ligands: MG.13, ATP.14, GT0.24 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.84, B:V.231 Hydrogen bonds: B:G.20, B:T.47, B:G.232, B:G.232, B:T.233, B:T.233, B:G.234, B:D.235 Water bridges: B:Y.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gandhi, A.K. et al., Crystal structures of human pyridoxal kinase in complex with the neurotoxins, ginkgotoxin and theophylline: insights into pyridoxal kinase inhibition. Plos One (2012)

Release Date

2012-05-02

Peptides

Pyridoxal kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyridoxal kinase

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