SMTL ID : 3h3n.2 (1 other biounit)

Glycerol Kinase H232R with Glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: Q.83, R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 Ligands: PO4.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.84, A:R.84, A:R.84, A:E.85, A:Y.136, A:Q.247 GOL.6: 9 residues within 4Å: Chain B: Q.83, R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 Ligands: PO4.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.84, B:R.84, B:R.84, B:Y.136, B:Q.247 GOL.11: 9 residues within 4Å: Chain C: Q.83, R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 Ligands: PO4.15 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.84, C:R.84, C:R.84, C:E.85, C:Y.136, C:Q.247 GOL.16: 9 residues within 4Å: Chain D: Q.83, R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 Ligands: PO4.20 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.84, D:R.84, D:R.84, D:Y.136, D:Q.247

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 10 residues within 4Å: Chain A: S.59, A.62, G.63, I.66 Chain B: S.59, A.62, G.63, I.66 Ligands: EDO.3, EDO.7 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:S.59, A:S.59 EDO.3: 4 residues within 4Å: Chain A: S.32, Q.33, S.59 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.59 EDO.4: 6 residues within 4Å: Chain A: W.54, Q.58, I.61, L.174, R.232, Y.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.234 EDO.7: 6 residues within 4Å: Chain B: S.32, Q.33, K.34, S.59, V.60 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.59 EDO.8: 6 residues within 4Å: Chain B: A.310, G.311, L.382, V.385, A.413, L.419 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.310, B:V.385 EDO.9: 5 residues within 4Å: Chain B: A.334, R.379, Q.383, L.418, F.422 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.383 EDO.12: 10 residues within 4Å: Chain C: S.59, A.62, G.63, I.66 Chain D: S.59, A.62, G.63, I.66 Ligands: EDO.13, EDO.17 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:S.59, C:S.59 EDO.13: 4 residues within 4Å: Chain C: S.32, Q.33, S.59 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.59 EDO.14: 6 residues within 4Å: Chain C: W.54, Q.58, I.61, L.174, R.232, Y.234 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.234 EDO.17: 6 residues within 4Å: Chain D: S.32, Q.33, K.34, S.59, V.60 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.59 EDO.18: 6 residues within 4Å: Chain D: A.310, G.311, L.382, V.385, A.413, L.419 2 PLIP interactions: 2 interactions with chain D Water bridges: D:A.310, D:V.385 EDO.19: 5 residues within 4Å: Chain D: A.334, R.379, Q.383, L.418, F.422 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.383

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

PO4.5: 7 residues within 4Å: Chain A: G.13, T.14, T.15, D.246, G.267, T.268 Ligands: GOL.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.14, A:T.15, A:D.246, A:T.268, A:T.268 Water bridges: A:Q.247 PO4.10: 6 residues within 4Å: Chain B: G.13, T.14, T.15, G.267, T.268 Ligands: GOL.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.14, B:T.14, B:T.15, B:T.268, B:T.268 Water bridges: B:Q.247, B:Q.247, B:G.269, B:G.269 PO4.15: 7 residues within 4Å: Chain C: G.13, T.14, T.15, D.246, G.267, T.268 Ligands: GOL.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.14, C:T.15, C:D.246, C:T.268, C:T.268 Water bridges: C:Q.247 PO4.20: 6 residues within 4Å: Chain D: G.13, T.14, T.15, G.267, T.268 Ligands: GOL.16 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.14, D:T.14, D:T.15, D:T.268, D:T.268 Water bridges: D:Q.247, D:Q.247, D:G.269, D:G.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yeh, J.I. et al., Structural characterizations of glycerol kinase: unraveling phosphorylation-induced long-range activation. Biochemistry (2009)

Release Date

2009-06-02

Peptides

Glycerol kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
O

C
X

D
O

Glycerol kinase

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