SMTL ID : 3wid.1

Structure of a glucose dehydrogenase T277F mutant in complex with NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.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.11: 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.17: 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 NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 22 residues within 4Å: Chain A: 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 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:F.275 Hydrogen bonds: A:S.194, A:G.195, A:S.196, A:S.196, A:E.197, A:N.216, A:Y.238, A:T.252, A:D.255, A:T.258, A:T.258, A:F.275, 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 NAP.7: 24 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 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:F.275, B:F.277 Hydrogen bonds: B:S.194, B:G.195, B:S.196, B:S.196, B:E.197, B:N.216, B:T.252, B:T.252, B:T.258, B:F.277, B:D.306 Water bridges: B:S.196, B:S.196, B:E.197, B:A.198 Salt bridges: B:R.217, B:H.218, B:K.349, B:K.349 pi-Cation interactions: B:R.217 NAP.12: 23 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, T.258, F.275, G.276, F.277, S.304, V.305, D.306, K.349 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.275 Hydrogen bonds: C:S.194, C:G.195, C:S.196, C:E.197, C:N.216, C:Y.238, C:T.252, C:T.258, C:F.275, C:F.277, C:D.306 Water bridges: C:A.198 Salt bridges: C:R.217, C:H.218, C:K.349, C:K.349 NAP.18: 21 residues within 4Å: Chain B: V.295 Chain D: N.160, I.192, 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 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.275, D:F.277 Hydrogen bonds: D:S.194, D:G.195, D:S.196, D:S.196, D:E.197, D:N.216, D:T.252, D:D.255, D:T.258, D:F.275, D:F.277, D:D.306 Water bridges: D:A.198 Salt bridges: D:R.217, D:H.218

4 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.120, A:L.125 Hydrogen bonds: A:R.130, A:Y.134 PGO.8: 9 residues within 4Å: Chain B: R.95, A.120, L.125, H.126, F.128, R.130, I.133, Y.134, D.135 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.120, B:L.125, B:F.128 Hydrogen bonds: B:R.130, B:Y.134 Water bridges: B:R.130 PGO.13: 8 residues within 4Å: Chain C: R.95, A.120, L.125, H.126, F.128, R.130, I.133, Y.134 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.120, C:F.128 Hydrogen bonds: C:R.130, C:R.130, C:Y.134, C:Y.134 Water bridges: C:H.126 PGO.19: 7 residues within 4Å: Chain D: R.95, L.125, H.126, F.128, R.130, Y.134, D.135 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.128 Hydrogen bonds: D:R.95, D:H.126, D:R.130, D:Y.134

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

1PE.4: 10 residues within 4Å: Chain A: Y.82, I.137, L.140, V.141, K.142, K.309, V.313 Chain B: D.181, I.185, G.209 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.142, A:K.309, B:D.181, B:G.209 Water bridges: B:F.184, B:G.186 1PE.5: 8 residues within 4Å: Chain A: R.106, E.166 Chain B: K.173, Q.178, S.182 Chain C: K.173, R.174, S.175 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.106, A:K.173, B:K.173, B:Q.178 1PE.9: 11 residues within 4Å: Chain A: Q.178, S.182 Chain B: I.104, R.106, E.166, I.310, H.311, Q.314 Chain D: K.173, R.174, S.175 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain B Water bridges: A:Q.178, B:N.109, B:E.166 Hydrogen bonds: B:R.106, B:E.166, B:Q.314, B:Q.314 1PE.10: 12 residues within 4Å: Chain A: D.181, I.185 Chain B: I.137, Q.138, L.140, V.141, K.142, N.144, K.309, V.313, L.316, D.317 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.142, B:K.309, B:V.313 Water bridges: B:D.317 1PE.14: 13 residues within 4Å: Chain C: I.137, Q.138, L.140, V.141, K.142, N.144, K.309, V.313, L.316, D.317 Chain D: N.179, D.181, I.185 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.309, C:V.313, D:D.181 1PE.15: 14 residues within 4Å: Chain A: V.100 Chain B: K.173, R.174, S.175 Chain C: K.173, I.176, Q.178, N.179, S.182 Chain D: I.104, R.106, E.166, V.170 Ligands: 1PE.16 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:K.173, C:N.179, C:S.182, D:R.106 Water bridges: B:I.176 1PE.16: 16 residues within 4Å: Chain A: K.173, R.174, S.175 Chain B: V.100 Chain C: I.104, R.106, E.166, D.169, V.170 Chain D: K.173, I.176, Q.178, N.179, D.180, S.182 Ligands: 1PE.15 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Water bridges: A:I.176 Hydrogen bonds: C:I.104, C:R.106, D:S.182 1PE.20: 13 residues within 4Å: Chain C: D.181, I.185 Chain D: Y.82, I.137, Q.138, 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:V.313

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

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