SMTL ID : 3lq3.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 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.248, Q.250, N.253, D.270, Y.273, E.289, Y.294, F.301, W.359, W.362, E.373, F.374, Y.376, Y.379 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.294, A:Y.294, A:Y.294, A:F.374, A:F.374, A:F.374, A:F.374, A:Y.376 Hydrogen bonds: A:D.248, A:Q.250, A:N.253, A:Y.273 Salt bridges: A:D.248, A:E.289 pi-Cation interactions: A:F.301, A:W.359, A:W.359 HC7.8: 14 residues within 4Å: Chain B: D.248, Q.250, N.253, D.270, Y.273, E.289, Y.294, F.301, W.359, W.362, E.373, F.374, Y.376, Y.379 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.294, B:Y.294, B:Y.294, B:F.374, B:F.374, B:F.374, B:F.374, B:Y.376 Hydrogen bonds: B:D.248, B:Q.250, B:N.253 Water bridges: B:D.270 Salt bridges: B:D.248, B:E.289 pi-Cation interactions: B:F.301, B:W.359, B:W.359

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.253, D.270 Ligands: ADP.6, AMP.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.270, H2O.1, H2O.1 MG.9: 4 residues within 4Å: Chain B: N.253, D.270 Ligands: ADP.13, AMP.14 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.270, H2O.11, H2O.11

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

UNX.3: 5 residues within 4Å: Chain A: K.160, T.161, E.251, D.293, T.295 No protein-ligand interaction detected (PLIP) UNX.4: 4 residues within 4Å: Chain A: E.251, E.289, Y.292, Y.294 No protein-ligand interaction detected (PLIP) UNX.10: 5 residues within 4Å: Chain B: K.160, T.161, E.251, D.293, T.295 No protein-ligand interaction detected (PLIP) UNX.11: 4 residues within 4Å: Chain B: E.251, E.289, Y.292, Y.294 No protein-ligand interaction detected (PLIP)

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

SO4.5: 3 residues within 4Å: Chain A: H.317, R.320, H.321 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:H.317, A:R.320, A:H.321 SO4.12: 3 residues within 4Å: Chain B: H.317, R.320, H.321 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.317, B:R.320, B:H.321

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

ADP.6: 15 residues within 4Å: Chain A: L.88, L.108, R.110, P.139, E.151, Q.152, Y.153, I.154, P.158, G.252, N.253, L.255, D.270 Ligands: MG.2, AMP.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.110, A:Q.152, A:I.154, A:D.270 Water bridges: A:R.110, A:R.110, A:N.253 Salt bridges: A:R.110 ADP.13: 15 residues within 4Å: Chain B: L.88, L.108, R.110, P.139, E.151, Q.152, Y.153, I.154, P.158, G.252, N.253, L.255, D.270 Ligands: MG.9, AMP.14 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.110, B:E.151, B:Q.152, B:I.154, B:D.270, B:D.270 Water bridges: B:R.110, B:R.110, B:N.253, B:E.272 Salt bridges: B:R.110

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 14 residues within 4Å: Chain A: V.80, L.88, L.108, R.110, P.139, E.151, Q.152, Y.153, I.154, P.158, G.252, L.255 Ligands: MG.2, ADP.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.110, A:Q.152, A:I.154 AMP.14: 14 residues within 4Å: Chain B: V.80, L.88, L.108, R.110, P.139, E.151, Q.152, Y.153, I.154, P.158, G.252, L.255 Ligands: MG.9, ADP.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.110, B:E.151, B:Q.152, B:I.154

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

2010-05-05

Peptides

Choline/ethanolamine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Choline/ethanolamine kinase

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