SMTL ID : 3vgm.1

Crystal structure of a ROK family glucokinase from Streptomyces griseus in complex with glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-tetramer

Ligands

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.1: 12 residues within 4Å: Chain A: A.65, G.66, Y.67, N.104, D.105, A.106, G.133, L.134, G.135, E.154, H.157, E.176 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.66, A:N.104, A:N.104, A:A.106, A:L.134, A:E.154, A:E.154 Water bridges: A:Y.67, A:D.105, A:G.133, A:G.133, A:G.135 Salt bridges: A:H.157 BGC.4: 12 residues within 4Å: Chain B: A.65, G.66, Y.67, N.104, D.105, A.106, G.133, L.134, G.135, E.154, H.157, E.176 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.66, B:N.104, B:N.104, B:A.106, B:L.134, B:E.154, B:E.154 Water bridges: B:Y.67, B:D.105, B:G.133, B:G.133, B:G.135 Salt bridges: B:H.157 BGC.7: 12 residues within 4Å: Chain C: A.65, G.66, Y.67, N.104, D.105, A.106, G.133, L.134, G.135, E.154, H.157, E.176 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.66, C:N.104, C:N.104, C:A.106, C:L.134, C:E.154, C:E.154 Water bridges: C:D.105, C:G.133, C:G.133, C:G.135 Salt bridges: C:H.157 BGC.10: 12 residues within 4Å: Chain D: A.65, G.66, Y.67, N.104, D.105, A.106, G.133, L.134, G.135, E.154, H.157, E.176 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.66, D:N.104, D:N.104, D:A.106, D:L.134, D:E.154, D:E.154 Water bridges: D:D.105, D:G.133, D:G.133, D:G.135 Salt bridges: D:H.157

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.157, C.167, C.169, C.174 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.157, A:C.167, A:C.169, A:C.174 ZN.5: 4 residues within 4Å: Chain B: H.157, C.167, C.169, C.174 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.157, B:C.167, B:C.169, B:C.174 ZN.8: 4 residues within 4Å: Chain C: H.157, C.167, C.169, C.174 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.157, C:C.167, C:C.169, C:C.174 ZN.11: 4 residues within 4Å: Chain D: H.157, C.167, C.169, C.174 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.157, D:C.167, D:C.169, D:C.174

4 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: N.104, N.107, G.136, A.152, A.153 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.136, A:A.153, H2O.1, H2O.1 K.6: 5 residues within 4Å: Chain B: N.104, N.107, G.136, A.152, A.153 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.136, B:A.153, H2O.10, H2O.11 K.9: 5 residues within 4Å: Chain C: N.104, N.107, G.136, A.152, A.153 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:G.136, C:A.153, H2O.20, H2O.20 K.12: 5 residues within 4Å: Chain D: N.104, N.107, G.136, A.152, A.153 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:G.136, D:A.153, H2O.30, H2O.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyazono, K. et al., Substrate recognition mechanism and substrate-dependent conformational changes of an ROK family glucokinase from Streptomyces griseus. J.Bacteriol. (2012)

Release Date

2011-12-07

Peptides

Glucokinase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glucokinase

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