SMTL ID : 3wic.1

Structure of a substrate/cofactor-unbound glucose dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.41, H.68, E.69, E.156 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.41, A:H.68, A:E.69 ZN.2: 4 residues within 4Å: Chain A: C.99, C.102, C.110, D.116 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.110, A:D.116 ZN.6: 4 residues within 4Å: Chain B: C.41, H.68, E.69, E.156 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.41, B:H.68, B:E.69, H2O.3 ZN.7: 4 residues within 4Å: Chain B: C.99, C.102, C.110, D.116 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.99, B:C.102, B:C.110, B:D.116 ZN.13: 4 residues within 4Å: Chain C: C.41, H.68, E.69, E.156 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.41, C:H.68, C:E.69 ZN.14: 4 residues within 4Å: Chain C: C.99, C.102, C.110, D.116 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.99, C:C.102, C:C.110, C:D.116 ZN.18: 4 residues within 4Å: Chain D: C.41, H.68, E.69, E.156 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.41, D:H.68, D:E.69 ZN.19: 4 residues within 4Å: Chain D: C.99, C.102, C.110, D.116 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.99, D:C.102, D:C.110, D:D.116

6 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.3: 7 residues within 4Å: Chain A: R.95, A.120, L.125, H.126, R.130, I.133, Y.134 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.120, A:L.125 Hydrogen bonds: A:R.130, A:Y.134, A:Y.134 PGO.8: 8 residues within 4Å: Chain B: R.95, A.120, L.125, H.126, R.130, I.133, Y.134, D.135 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.120, B:L.125 Hydrogen bonds: B:R.130, B:Y.134, B:Y.134 PGO.9: 7 residues within 4Å: Chain B: F.88, V.143, D.145, P.146, D.147, L.148, G.149 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.88 Hydrogen bonds: B:P.146, B:L.148, B:G.149 PGO.15: 7 residues within 4Å: Chain C: R.95, L.125, H.126, R.130, I.133, Y.134, D.135 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.125 Hydrogen bonds: C:R.130, C:R.130, C:Y.134, C:Y.134 PGO.20: 8 residues within 4Å: Chain D: R.95, A.120, L.125, H.126, F.128, R.130, Y.134, D.135 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.120, D:F.128 Hydrogen bonds: D:R.130, D:Y.134 Water bridges: D:R.130 PGO.21: 6 residues within 4Å: Chain D: F.88, V.143, D.145, P.146, L.148, G.149 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.88, D:V.143 Hydrogen bonds: D:P.146, D:L.148, D:G.149

8 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 9 residues within 4Å: Chain A: I.104, R.106, E.166, V.170, I.310 Chain B: Q.178 Chain C: K.173, R.174, S.175 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:R.106, A:E.166, A:E.166, B:Q.178 Water bridges: B:K.173, C:I.176 1PE.5: 10 residues within 4Å: Chain A: Y.82, I.137, L.140, V.141, K.142, N.144, K.309, V.313 Chain B: D.181, I.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.142, A:K.309 1PE.10: 8 residues within 4Å: Chain A: Q.178 Chain B: R.106, E.166, H.311, Q.314 Chain D: K.173, R.174, S.175 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.106, B:Q.314, B:Q.314 1PE.11: 10 residues within 4Å: Chain A: I.185 Chain B: Y.82, I.137, Q.138, L.140, V.141, K.142, N.144, K.309, V.313 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.30, B:K.142, B:N.144, B:K.309 1PE.12: 11 residues within 4Å: Chain B: K.173, R.174 Chain C: K.173, I.176, Q.178, N.179, S.182 Chain D: I.104, R.106, E.166, V.170 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:I.104, C:K.173 Water bridges: B:I.176 1PE.16: 10 residues within 4Å: Chain A: K.173, R.174 Chain C: I.104, R.106, K.173 Chain D: K.173, I.176, Q.178, N.179, S.182 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.104, C:K.173, C:K.173, D:S.182 Water bridges: C:R.106 1PE.17: 12 residues within 4Å: Chain C: Y.82, I.137, Q.138, L.140, V.141, K.142, N.144, K.309, V.313 Chain D: N.179, D.181, I.185 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.82, C:Y.82, C:K.142, C:K.309 Water bridges: D:K.206, D:G.209 1PE.22: 13 residues within 4Å: Chain C: N.179, D.181, I.185 Chain D: Y.82, I.137, L.140, V.141, K.142, N.144, K.309, V.313, L.316, D.317 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.142, D:K.309, D:D.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanoh, Y. et al., Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-05-14

Peptides

Glucose 1-dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucose 1-dehydrogenase