SMTL ID : 3g25.3 (2 other biounits)

1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: Q.84, R.85, E.86, W.105, Y.137, D.247, Q.248, F.272 Ligands: PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.85, A:R.85, A:E.86, A:Y.137, A:D.247, A:Q.248 GOL.3: 10 residues within 4Å: Chain B: T.15, Q.84, R.85, E.86, W.105, Y.137, D.247, Q.248, F.272 Ligands: PO4.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.85, B:R.85, B:Y.137, B:Y.137, B:D.247, B:Q.248

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

PO4.2: 7 residues within 4Å: Chain A: G.14, T.15, T.16, R.19, G.268, T.269 Ligands: GOL.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.15, A:T.15, A:T.16, A:R.19, A:T.269, A:T.269 PO4.6: 6 residues within 4Å: Chain B: G.14, T.15, G.268, T.269 Ligands: GOL.3, NA.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.15, B:T.15, B:T.269, B:T.269 Salt bridges: B:R.19 PO4.7: 4 residues within 4Å: Chain A: R.323 Chain B: Y.334, R.337, K.375 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.334, B:R.337 Water bridges: B:K.375 Salt bridges: B:K.375, A:R.323 PO4.8: 4 residues within 4Å: Chain A: Y.334, K.375 Chain B: R.323 Ligands: NA.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.334 Salt bridges: A:K.375, B:R.323

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 7 residues within 4Å: Chain B: G.14, T.15, T.16, S.17, R.19, T.269 Ligands: PO4.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.15, B:T.16, B:S.17, B:R.19, B:R.19, B:T.269 NA.5: 3 residues within 4Å: Chain A: K.375 Chain B: R.323 Ligands: PO4.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol. TO BE PUBLISHED

Release Date

2009-02-17

Peptides

Glycerol kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Glycerol kinase

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