SMTL ID : 3ay6.1

Crystal structure of Bacillus megaterium glucose dehydrogenase 4 A258F mutant in complex with NADH and D-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 28 residues within 4Å: Chain A: G.22, T.25, G.26, L.27, N.45, Y.47, G.72, D.73, V.74, N.100, A.101, G.102, V.103, T.123, M.151, S.152, S.153, Y.166, K.170, P.196, G.197, A.198, M.199, T.201, P.202, I.203, N.204 Ligands: BGC.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.196 Hydrogen bonds: A:T.25, A:T.25, A:T.25, A:L.27, A:D.73, A:V.74, A:N.100, A:G.102, A:K.170, A:M.199, A:M.199, A:T.201, A:I.203, A:N.204 Water bridges: A:G.28, A:N.100 NAI.5: 27 residues within 4Å: Chain B: G.22, T.25, G.26, L.27, Y.47, G.72, D.73, V.74, N.100, A.101, G.102, V.103, T.123, M.151, S.152, S.153, Y.166, K.170, P.196, G.197, A.198, M.199, T.201, P.202, I.203, N.204 Ligands: BGC.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:P.196 Hydrogen bonds: B:T.25, B:T.25, B:T.25, B:L.27, B:D.73, B:V.74, B:N.100, B:G.102, B:K.170, B:M.199, B:M.199, B:T.201, B:I.203, B:N.204 Water bridges: B:G.28, B:N.48, B:N.100 NAI.7: 28 residues within 4Å: Chain C: G.22, T.25, G.26, L.27, N.45, Y.47, G.72, D.73, V.74, N.100, A.101, G.102, V.103, T.123, M.151, S.152, S.153, Y.166, K.170, P.196, G.197, A.198, M.199, T.201, P.202, I.203, N.204 Ligands: BGC.8 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:P.196 Hydrogen bonds: C:T.25, C:T.25, C:T.25, C:L.27, C:D.73, C:D.73, C:V.74, C:N.100, C:G.102, C:Y.166, C:K.170, C:M.199, C:M.199, C:T.201, C:I.203, C:N.204 Water bridges: C:G.28, C:Y.47, C:N.100 NAI.10: 29 residues within 4Å: Chain D: G.22, T.25, G.26, L.27, N.45, Y.47, G.72, D.73, V.74, T.75, N.100, A.101, G.102, V.103, T.123, M.151, S.152, S.153, Y.166, K.170, P.196, G.197, A.198, M.199, T.201, P.202, I.203, N.204 Ligands: BGC.9 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:P.196 Hydrogen bonds: D:T.25, D:T.25, D:L.27, D:D.73, D:D.73, D:V.74, D:N.100, D:G.102, D:Y.166, D:K.170, D:M.199, D:M.199, D:I.203, D:N.204 Water bridges: D:N.100

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

BGC.2: 14 residues within 4Å: Chain A: E.104, S.153, H.155, W.160, Y.166, G.197, A.198, I.203, N.204, K.207, M.258 Chain C: F.264, G.269 Ligands: NAI.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.104, A:E.104, A:S.153, A:Y.166, A:Y.166, A:N.204, A:K.207, A:K.207 Water bridges: A:E.104 Salt bridges: A:H.155 BGC.4: 13 residues within 4Å: Chain B: E.104, S.153, H.155, W.160, Y.166, A.198, I.203, N.204, K.207, M.258 Chain D: F.264, G.269 Ligands: NAI.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.104, B:E.104, B:S.153, B:Y.166, B:Y.166, B:N.204, B:K.207, B:K.207 Salt bridges: B:H.155 BGC.8: 13 residues within 4Å: Chain A: F.264, G.269 Chain C: E.104, S.153, H.155, W.160, Y.166, A.198, I.203, N.204, K.207, M.258 Ligands: NAI.7 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.104, C:E.104, C:S.153, C:Y.166, C:N.204, C:K.207, C:K.207, A:G.269 Salt bridges: C:H.155 BGC.9: 13 residues within 4Å: Chain B: F.264, G.269 Chain D: E.104, S.153, H.155, W.160, Y.166, A.198, I.203, N.204, K.207, M.258 Ligands: NAI.10 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:E.104, D:E.104, D:S.153, D:Y.166, D:N.204, D:K.207, D:K.207, B:G.269 Salt bridges: D:H.155

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

CL.3: 6 residues within 4Å: Chain A: Y.261, P.262, S.263 Chain C: Y.261, P.262, S.263 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain B: Y.261, P.262, S.263 Chain D: Y.261, P.262, S.263 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishioka, T. et al., Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV. Febs J. (2012)

Release Date

2012-05-23

Peptides

Glucose 1-dehydrogenase 4: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucose 1-dehydrogenase 4