SMTL ID : 3feg.1

Crystal structure of human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x HC7: (2S)-2-[4'-({dimethyl[2-(phosphonooxy)ethyl]ammonio}acetyl)biphenyl-4-yl]-2-hydroxy-4,4-dimethylmorpholin-4-ium(Non-covalent)

HC7.1: 14 residues within 4Å: Chain A: D.226, Q.228, N.231, D.248, Y.251, E.267, Y.272, F.279, W.337, W.340, E.351, F.352, Y.354, Y.357 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.272, A:Y.272, A:Y.272, A:F.352, A:F.352, A:F.352, A:F.352, A:Y.354 Hydrogen bonds: A:D.226, A:Q.228, A:N.231, A:Y.251 Salt bridges: A:D.226, A:E.267 pi-Cation interactions: A:F.279, A:W.337, A:W.337 HC7.8: 14 residues within 4Å: Chain B: D.226, Q.228, N.231, D.248, Y.251, E.267, Y.272, F.279, W.337, W.340, E.351, F.352, Y.354, Y.357 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.272, B:Y.272, B:Y.272, B:F.352, B:F.352, B:F.352, B:F.352, B:Y.354 Hydrogen bonds: B:D.226, B:Q.228, B:N.231 Water bridges: B:D.248 Salt bridges: B:D.226, B:E.267 pi-Cation interactions: B:F.279, B:W.337, B:W.337

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

SO4.2: 3 residues within 4Å: Chain A: H.295, R.298, H.299 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.295, A:R.298, A:H.299 SO4.9: 3 residues within 4Å: Chain B: H.295, R.298, H.299 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.295, B:R.298, B:H.299

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

ADP.3: 16 residues within 4Å: Chain A: L.66, L.86, R.88, P.117, E.129, Q.130, Y.131, I.132, P.136, G.230, N.231, L.233, V.247, D.248 Ligands: AMP.4, MG.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.88, A:I.132, A:G.230 Water bridges: A:N.231, A:D.248, A:D.248, A:F.249 Salt bridges: A:R.88 ADP.10: 16 residues within 4Å: Chain B: L.66, L.86, R.88, P.117, E.129, Q.130, Y.131, I.132, P.136, G.230, N.231, L.233, V.247, D.248 Ligands: AMP.11, MG.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.88, B:E.129, B:I.132, B:G.230, B:D.248 Water bridges: B:N.231, B:D.248, B:D.248, B:F.249, B:E.250 Salt bridges: B:R.88

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 13 residues within 4Å: Chain A: V.58, L.66, L.86, R.88, P.117, E.129, Q.130, Y.131, I.132, P.136, G.230, L.233 Ligands: ADP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.88, A:E.129, A:I.132, A:G.230 AMP.11: 13 residues within 4Å: Chain B: V.58, L.66, L.86, R.88, P.117, E.129, Q.130, Y.131, I.132, P.136, G.230, L.233 Ligands: ADP.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.88, B:E.129, B:E.129, B:I.132, B:G.230

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: N.231, D.248 Ligands: ADP.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.248, H2O.10, H2O.11, H2O.11 MG.12: 3 residues within 4Å: Chain B: N.231, D.248 Ligands: ADP.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.248, H2O.21, H2O.23, H2O.23

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

UNX.6: 4 residues within 4Å: Chain A: E.229, E.267, Y.270, Y.272 No protein-ligand interaction detected (PLIP) UNX.7: 1 residues within 4Å: Chain A: F.165 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain B: E.229, E.267, Y.270, Y.272 No protein-ligand interaction detected (PLIP) UNX.14: 1 residues within 4Å: Chain B: F.165 No protein-ligand interaction detected (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

2008-12-23

Peptides

Choline/ethanolamine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Choline/ethanolamine kinase