SMTL ID : 3h45.1 (2 other biounits)

Glycerol Kinase H232E with Ethylene Glycol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

3 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: PO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.84, A:R.84, A:Y.136, A:Q.247 EDO.2: 2 residues within 4Å: Chain A: H.126, E.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.127 EDO.6: 8 residues within 4Å: Chain B: R.84, E.85, W.104, Y.136, D.246, Q.247, F.271 Ligands: PO4.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.84, B:Y.136, B:D.246, B:Q.247

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

PO4.3: 5 residues within 4Å: Chain A: G.13, T.14, G.267, T.268 Ligands: EDO.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.14, A:T.14, A:T.268 Water bridges: A:S.16, A:S.16, A:D.246, A:D.246, A:G.267, A:G.269, A:G.269 PO4.4: 7 residues within 4Å: Chain A: S.59, A.62, G.63, I.66 Chain B: S.59, A.62, G.63 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.59, B:G.63 PO4.5: 7 residues within 4Å: Chain A: A.310, G.311, I.314, L.382, V.385, A.413, L.419 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.310, A:A.310 Water bridges: A:V.385, A:N.416 PO4.7: 4 residues within 4Å: Chain B: T.14, G.267, T.268 Ligands: EDO.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.14, B:T.14, B:T.14, B:D.246, B:T.268, B:T.268, B:T.268 Water bridges: B:Q.247, B:Q.247

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
O

Glycerol kinase

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