SMTL ID : 3ge1.1

2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with ADP and Glycerol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: G.14, T.15, T.16, R.19, Y.267, G.268, T.269, G.312, S.313, I.315, Q.316, A.328, P.329, G.412, G.413, A.414, K.416, N.417 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:T.15, A:T.16, A:T.269, A:T.269, A:Q.316, A:G.413, A:N.417 Water bridges: A:R.19, A:R.19, A:R.19, A:Q.34 Salt bridges: A:R.19, A:R.19 ADP.7: 17 residues within 4Å: Chain B: G.14, T.15, T.16, R.19, G.268, T.269, G.312, S.313, I.315, Q.316, A.328, P.329, G.413, A.414, K.416, N.417, I.420 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.15, B:T.15, B:T.16, B:T.269, B:Q.316, B:G.413, B:N.417 Water bridges: B:Q.316 Salt bridges: B:R.19, B:R.19 ADP.11: 16 residues within 4Å: Chain C: G.14, T.15, T.16, R.19, G.268, T.269, G.312, S.313, I.315, Q.316, A.328, P.329, G.413, A.414, N.417 Ligands: GOL.12 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:T.15, C:T.15, C:T.16, C:T.269, C:Q.316, C:Q.316, C:G.413, C:N.417 Water bridges: C:D.12, C:R.19 Salt bridges: C:R.19, C:R.19 ADP.15: 16 residues within 4Å: Chain D: G.14, T.15, T.16, R.19, G.268, T.269, G.312, S.313, I.315, Q.316, A.328, P.329, G.413, A.414, K.416, N.417 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.15, D:T.15, D:T.15, D:T.16, D:T.269, D:T.269, D:Q.316, D:G.413, D:N.417 Water bridges: D:R.19, D:D.247, D:Q.316 Salt bridges: D:R.19, D:R.19

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Q.84, R.85, E.86, W.105, Y.137, D.247, Q.248, F.272 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.85, A:R.85, A:E.86, A:D.247, A:Q.248 GOL.8: 9 residues within 4Å: Chain B: T.15, R.85, E.86, W.105, Y.137, R.190, D.247, Q.248, F.272 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.85, B:R.85, B:Y.137, B:R.190, B:D.247, B:Q.248 GOL.12: 10 residues within 4Å: Chain C: T.15, Q.84, R.85, E.86, W.105, Y.137, D.247, Q.248, F.272 Ligands: ADP.11 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.85, C:R.85, C:E.86, C:Y.137, C:D.247, C:Q.248 GOL.16: 10 residues within 4Å: Chain D: T.15, Q.84, R.85, E.86, W.105, Y.137, R.190, D.247, Q.248, F.272 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:T.15, D:T.15, D:R.85, D:R.85, D:Y.137, D:Y.137, D:R.190, D:D.247, D:Q.248

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

PO4.3: 3 residues within 4Å: Chain A: R.323 Chain B: Y.334, K.375 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.334 Salt bridges: B:K.375, A:R.323 PO4.4: 3 residues within 4Å: Chain A: Y.334, K.375 Chain B: R.323 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.375, B:R.323 PO4.5: 7 residues within 4Å: Chain A: W.173, K.174, G.177, K.178, I.230, Y.232, H.233 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.174, A:H.233 PO4.9: 6 residues within 4Å: Chain B: K.174, G.177, K.178, I.230, Y.232, H.233 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.232 Salt bridges: B:K.174, B:K.178, B:H.233 PO4.13: 6 residues within 4Å: Chain C: K.174, G.177, K.178, I.230, Y.232, H.233 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.232 Water bridges: C:K.174, C:K.178 Salt bridges: C:K.174, C:H.233 PO4.17: 3 residues within 4Å: Chain C: R.323 Chain D: Y.334, K.375 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.334, C:R.323 Salt bridges: D:K.375, C:R.323 PO4.18: 4 residues within 4Å: Chain C: Y.334, R.337, K.375 Chain D: R.323 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.337 Salt bridges: C:K.375, D:R.323 PO4.19: 6 residues within 4Å: Chain D: K.174, G.177, K.178, I.230, Y.232, H.233 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.232 Water bridges: D:K.174 Salt bridges: D:K.174, D:H.233

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: S.340, T.341, R.380, E.384 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: S.340, T.341, E.384 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: S.340, T.341, R.380, E.384, L.484 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: S.340, T.341, R.380, E.384 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with ADP and Glycerol. To be Published

Release Date

2009-03-24

Peptides

Glycerol kinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glycerol kinase

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