SMTL ID : 3g15.1

Crystal structure of human choline kinase alpha in complex with hemicholinium-3 and ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: R.61, L.68, L.88, R.90, P.138, Q.151, F.152, I.153, R.157, G.254, N.255, L.257, I.273, D.274, E.276 Ligands: MG.2, SO4.4, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.90, A:Q.151, A:I.153 Water bridges: A:R.157, A:G.254, A:D.274 Salt bridges: A:R.61, A:R.90, A:R.90 ADP.18: 16 residues within 4Å: Chain B: L.68, L.88, R.90, P.138, Q.151, F.152, I.153, R.157, G.254, N.255, I.273, D.274, E.276 Ligands: MG.19, SO4.21, MG.22 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.90, B:Q.151, B:I.153 Water bridges: B:G.254, B:N.255, B:D.274 Salt bridges: B:R.90, B:R.90

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: N.255, D.274 Ligands: ADP.1, SO4.4, MG.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.274, H2O.1 MG.5: 5 residues within 4Å: Chain A: D.274, E.276 Ligands: ADP.1, MG.2, SO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.274, A:D.274, A:E.276, H2O.1 MG.19: 5 residues within 4Å: Chain B: N.255, D.274 Ligands: ADP.18, SO4.21, MG.22 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.274, H2O.7 MG.22: 5 residues within 4Å: Chain B: D.274, E.276 Ligands: ADP.18, MG.19, SO4.21 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.274, B:D.274, B:E.276, H2O.7

2 x HC6: (2S,2'S)-2,2'-biphenyl-4,4'-diylbis(2-hydroxy-4,4-dimethylmorpholin-4-ium)(Non-covalent)

HC6.3: 14 residues within 4Å: Chain A: D.250, Q.252, Y.277, E.293, Y.298, F.305, W.364, W.367, I.377, E.378, F.379, Y.384 Ligands: SO4.4, UNX.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.367, A:I.377, A:F.379, A:F.379, A:F.379, A:F.379 Hydrogen bonds: A:Q.252, A:E.293 Salt bridges: A:D.250, A:E.378 pi-Stacking: A:Y.298 pi-Cation interactions: A:F.305, A:W.364, A:W.367 HC6.20: 13 residues within 4Å: Chain B: D.250, Q.252, Y.277, E.293, Y.298, F.305, W.364, W.367, I.377, E.378, F.379, Y.384 Ligands: SO4.21 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:W.367, B:I.377, B:F.379, B:F.379 Hydrogen bonds: B:E.293 Salt bridges: B:D.250 pi-Stacking: B:Y.298 pi-Cation interactions: B:F.305, B:W.364, B:W.367

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

SO4.4: 9 residues within 4Å: Chain A: D.250, Q.252, N.255, D.274, E.276 Ligands: ADP.1, MG.2, HC6.3, MG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.252, A:N.255 SO4.21: 9 residues within 4Å: Chain B: D.250, Q.252, N.255, D.274, E.276 Ligands: ADP.18, MG.19, HC6.20, MG.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.252, B:N.255 Water bridges: B:Y.277

21 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.6: 4 residues within 4Å: Chain A: E.253, E.293, Y.296, Y.298 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: E.28, P.29, R.30 Ligand excluded by PLIP UNX.8: 5 residues within 4Å: Chain A: Y.298, S.299, Y.300, F.305 Ligands: HC6.3 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: R.214, Y.381, M.382 Ligands: UNX.10 Ligand excluded by PLIP UNX.10: 7 residues within 4Å: Chain A: K.217, Y.303, G.380, Y.381, M.382, D.383 Ligands: UNX.9 Ligand excluded by PLIP UNX.11: 6 residues within 4Å: Chain A: Y.92, M.121, I.143, F.144, G.147, R.148 Ligand excluded by PLIP UNX.12: 7 residues within 4Å: Chain A: H.248, D.250, D.274, F.275, E.276, Y.277, S.278 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: P.27, E.28, T.31 Ligand excluded by PLIP UNX.14: 6 residues within 4Å: Chain A: F.128, L.131, A.132, G.137, P.138, F.275 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: D.159, T.160, E.161 Ligand excluded by PLIP UNX.16: 1 residues within 4Å: Chain A: L.399 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: R.48 Chain B: K.188 Ligand excluded by PLIP UNX.23: 4 residues within 4Å: Chain B: E.253, E.293, Y.296, Y.298 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain B: R.156, R.157 Ligand excluded by PLIP UNX.25: 3 residues within 4Å: Chain B: L.165, P.166, D.167 Ligand excluded by PLIP UNX.26: 4 residues within 4Å: Chain B: F.209, T.210, E.211, R.214 Ligand excluded by PLIP UNX.27: 4 residues within 4Å: Chain B: K.208, F.209, I.215, L.218 Ligand excluded by PLIP UNX.28: 3 residues within 4Å: Chain B: R.214, Y.381, M.382 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain B: N.309 Ligand excluded by PLIP UNX.30: 4 residues within 4Å: Chain B: P.190, K.191, L.193, F.194 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain B: S.299, Y.300, E.301 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, B.S. et al., Crystal structures of human choline kinase isoforms in complex with hemicholinium-3: single amino acid near the active site influences inhibitor sensitivity. J.Biol.Chem. (2010)

Release Date

2009-02-10

Peptides

Choline kinase alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Choline kinase alpha

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