SMTL ID : 3h3o.3 (2 other biounits)

Glycerol Kinase H232R with Ethylene Glycol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.84, A:Y.136, A:Y.136, A:D.246, A:Q.247 EDO.5: 7 residues within 4Å: Chain B: R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.84, B:Y.136, B:Y.136, B:D.246, B:Q.247 EDO.6: 7 residues within 4Å: Chain B: W.104, Q.105, S.106, R.107, Y.136, F.308, T.350 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.104, B:R.107, B:T.350, B:T.350 EDO.7: 3 residues within 4Å: Chain B: Y.39, N.49, N.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.49, B:N.100 EDO.8: 5 residues within 4Å: Chain B: Y.193, L.198, E.199, W.200, V.218 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.193, B:Y.193, B:W.200 EDO.9: 8 residues within 4Å: Chain B: F.308, V.309, P.347, A.348, F.349, T.350, G.351, Q.388 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.309, B:T.350, B:T.350, B:Q.388 EDO.12: 8 residues within 4Å: Chain C: R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 Ligands: PO4.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.84, C:E.85, C:Y.136, C:Q.247 EDO.13: 2 residues within 4Å: Chain C: N.296, K.298 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.298, C:K.298 EDO.14: 6 residues within 4Å: Chain C: S.59, A.62, G.63 Chain D: S.59, A.62, G.63 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.59, C:S.59 EDO.16: 7 residues within 4Å: Chain D: R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.84, D:R.84, D:Q.247

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

PO4.2: 6 residues within 4Å: Chain A: G.13, T.14, R.18, G.267, T.268 Ligands: EDO.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.14, A:T.14, A:T.14, A:T.15, A:T.268, A:T.268 Water bridges: A:R.18 Salt bridges: A:R.18 PO4.3: 7 residues within 4Å: Chain A: W.104, Q.105, S.106, R.107, Y.136, F.308, T.350 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.104, A:W.104, A:T.350 Salt bridges: A:R.107 PO4.4: 5 residues within 4Å: Chain A: R.107, S.110, T.350, S.359, R.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.110 Salt bridges: A:R.107, A:R.362 PO4.10: 4 residues within 4Å: Chain B: G.13, T.14, G.267, T.268 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.14, B:T.14, B:T.268, B:T.268 Water bridges: B:G.269 PO4.11: 10 residues within 4Å: Chain B: R.107, D.134, F.308, T.350, G.351, L.352, G.353, W.357, D.358, S.359 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.134 Salt bridges: B:R.107 PO4.15: 5 residues within 4Å: Chain C: G.13, T.14, G.267, T.268 Ligands: EDO.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.14, C:T.268, C:T.268, C:T.268 PO4.17: 4 residues within 4Å: Chain D: G.13, T.14, G.267, T.268 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.14, D:T.14, D:T.268, D:T.268, D:T.268

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
O

B
X

C
B

D
C

Glycerol kinase

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