SMTL ID : 3wie.1

Structure of a glucose dehydrogenase T277F mutant in complex with D-glucose and NAADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 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 Ligands: BGC.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.41, A:H.68, A:E.69, H2O.3 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.5: 4 residues within 4Å: Chain B: C.41, H.68, E.69 Ligands: BGC.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.41, B:H.68, B:E.69, H2O.5 ZN.6: 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.9: 4 residues within 4Å: Chain C: C.41, H.68, E.69 Ligands: BGC.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.41, C:H.68, C:E.69, H2O.7 ZN.10: 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.13: 4 residues within 4Å: Chain D: C.41, H.68, E.69 Ligands: BGC.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.41, D:H.68, D:E.69, H2O.9 ZN.14: 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

4 x DN4: [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(3-carboxypyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate(Non-covalent)

DN4.3: 24 residues within 4Å: Chain A: T.43, N.160, I.192, G.193, S.194, G.195, S.196, E.197, N.216, R.217, H.218, Y.238, T.252, S.253, D.255, T.258, F.275, G.276, F.277, S.304, V.305, D.306 Chain C: V.295 Ligands: BGC.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.275 Hydrogen bonds: A:T.43, A:N.160, A:S.194, A:G.195, A:S.196, A:S.196, A:E.197, A:N.216, A:Y.238, A:D.255, A:T.258, A:T.258, A:F.277, A:D.306 Water bridges: A:S.196, A:A.198, A:T.252, A:K.355 Salt bridges: A:R.217, A:H.218 pi-Cation interactions: A:R.217 DN4.7: 25 residues within 4Å: Chain B: C.41, N.160, I.192, G.193, S.194, G.195, S.196, E.197, N.216, R.217, H.218, Y.238, T.252, S.253, D.255, T.258, F.275, G.276, F.277, S.304, V.305, D.306, K.349 Chain D: V.295 Ligands: BGC.8 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.275 Hydrogen bonds: B:T.43, B:N.160, B:S.194, B:G.195, B:S.196, B:S.196, B:E.197, B:N.216, B:Y.238, B:T.252, B:T.252, B:F.277, B:D.306 Salt bridges: B:R.217, B:H.218, B:K.349, B:K.349 pi-Cation interactions: B:R.217 DN4.11: 24 residues within 4Å: Chain A: V.295 Chain C: N.160, I.192, G.193, S.194, G.195, S.196, E.197, V.215, N.216, R.217, H.218, Y.238, T.252, S.253, D.255, T.258, F.275, G.276, F.277, S.304, V.305, D.306 Ligands: BGC.12 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.275 Hydrogen bonds: C:T.43, C:N.160, C:S.194, C:S.196, C:E.197, C:A.198, C:N.216, C:N.216, C:Y.238, C:T.252, C:T.258, C:T.258, C:F.277, C:D.306 Water bridges: C:G.195, C:S.196 Salt bridges: C:R.217, C:H.218 pi-Cation interactions: C:R.217 DN4.15: 24 residues within 4Å: Chain B: V.295 Chain D: C.41, N.160, I.192, G.193, S.194, G.195, S.196, E.197, N.216, R.217, H.218, Y.238, T.252, S.253, D.255, T.258, F.275, G.276, F.277, S.304, V.305, D.306 Ligands: BGC.16 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.275 Hydrogen bonds: D:N.160, D:S.194, D:S.196, D:S.196, D:E.197, D:N.216, D:R.217, D:T.252, D:T.252, D:D.255, D:T.258, D:F.277, D:D.306 Salt bridges: D:R.217, D:H.218 pi-Cation interactions: D:R.217

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

BGC.4: 14 residues within 4Å: Chain A: C.41, T.43, H.68, R.94, E.119, E.156, K.159, N.160, F.277, V.305, D.306 Chain C: E.296 Ligands: ZN.1, DN4.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.43, A:R.94, A:E.119, A:K.159, A:K.159, A:K.159, A:N.160, A:D.306 Water bridges: A:H.68, A:E.156 Salt bridges: A:H.68 BGC.8: 12 residues within 4Å: Chain B: T.43, H.68, V.93, R.94, E.119, E.156, K.159, N.160, D.306 Chain D: E.296 Ligands: ZN.5, DN4.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.94, B:E.156, B:K.159, B:K.159, B:K.159, B:N.160, B:D.306, B:D.306 Water bridges: B:E.197, B:E.197 Salt bridges: B:H.68 BGC.12: 11 residues within 4Å: Chain C: T.43, H.68, V.93, R.94, E.119, E.156, K.159, N.160, D.306 Ligands: ZN.9, DN4.11 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.94, C:K.159, C:K.159, C:K.159, C:N.160, C:D.306, C:D.306 Water bridges: C:H.68, C:E.156 Salt bridges: C:H.68 BGC.16: 13 residues within 4Å: Chain D: T.43, H.68, V.93, R.94, E.119, E.156, K.159, N.160, F.277, V.305, D.306 Ligands: ZN.13, DN4.15 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:T.43, D:R.94, D:E.119, D:K.159, D:K.159, D:K.159, D:N.160, D:D.306 Water bridges: D:H.68, D:E.156 Salt bridges: D:H.68

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

Related Entries With Identical Sequence