SMTL ID : 6xew.1

Structure of Serratia marcescens 2,3-butanediol dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 30 residues within 4Å: Chain A: G.25, N.28, G.29, M.30, D.49, W.50, A.51, I.72, D.73, V.74, N.100, A.101, G.102, V.103, V.123, T.149, A.150, S.151, Y.164, K.168, P.194, S.195, L.196, V.197, T.199, N.200, M.201, T.202 Ligands: HBR.3, HBS.4 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:P.194 Hydrogen bonds: A:G.25, A:G.27, A:M.30, A:W.50, A:D.73, A:D.73, A:V.74, A:N.100, A:G.102, A:K.168, A:V.197, A:T.199, A:N.200, A:M.201, A:T.202 Water bridges: A:N.28, A:N.28, A:G.29, A:G.31, A:N.100, A:N.200 pi-Stacking: A:W.50, A:W.50 NAD.2: 4 residues within 4Å: Chain A: W.50, A.51, K.52, N.200 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.50, A:W.50 Hydrogen bonds: A:K.52, A:N.200, A:N.200 Water bridges: A:N.28, A:A.51, A:E.53, A:E.53 NAD.6: 30 residues within 4Å: Chain C: G.25, N.28, G.29, M.30, D.49, W.50, A.51, I.72, D.73, V.74, N.100, A.101, G.102, V.103, V.123, T.149, A.150, S.151, Y.164, K.168, P.194, S.195, L.196, V.197, T.199, N.200, M.201, T.202 Ligands: HBR.8, HBS.9 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:P.194 Hydrogen bonds: C:G.25, C:G.27, C:M.30, C:W.50, C:D.73, C:V.74, C:N.100, C:G.102, C:Y.164, C:K.168, C:V.197, C:T.199, C:T.199, C:N.200, C:M.201, C:T.202 Water bridges: C:N.28, C:N.28, C:G.29, C:G.31, C:N.100, C:N.200 pi-Stacking: C:W.50, C:W.50 NAD.7: 4 residues within 4Å: Chain C: W.50, A.51, K.52, N.200 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.50, C:W.50 Hydrogen bonds: C:K.52, C:N.200, C:N.200 Water bridges: C:N.28, C:A.51, C:E.53, C:E.53, C:E.53

2 x HBR: R,3-HYDROXYBUTAN-2-ONE(Non-covalent)

HBR.3: 11 residues within 4Å: Chain A: H.104, S.151, S.153, Y.164, S.195, L.196, M.201, W.205 Chain C: Q.260 Ligands: NAD.1, HBS.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.205 Hydrogen bonds: A:S.151, A:S.153, A:Y.164, C:Q.260, C:Q.260 HBR.8: 11 residues within 4Å: Chain A: Q.260 Chain C: H.104, S.151, S.153, Y.164, S.195, L.196, M.201, W.205 Ligands: NAD.6, HBS.9 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Q.260, A:Q.260, C:S.151, C:S.153 Hydrophobic interactions: C:W.205

2 x HBS: S,3-HYDROXYBUTAN-2-ONE(Non-covalent)

HBS.4: 12 residues within 4Å: Chain A: H.104, S.151, S.153, Y.164, P.194, S.195, L.196, M.201, W.205 Chain C: Q.260 Ligands: NAD.1, HBR.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.151, A:S.153, A:Y.164, C:Q.260, C:Q.260 HBS.9: 12 residues within 4Å: Chain A: Q.260 Chain C: H.104, S.151, S.153, Y.164, P.194, S.195, L.196, M.201, W.205 Ligands: NAD.6, HBR.8 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.260, A:Q.260, C:S.151, C:S.153

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 12 residues within 4Å: Chain B: G.25, G.27, N.28, D.49, W.50, I.72, D.73, V.74, A.101, G.102, V.103, V.123 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.25, B:G.27, B:W.50, B:D.73, B:V.74, B:G.102 Water bridges: B:G.29 ADP.10: 12 residues within 4Å: Chain D: G.25, G.27, N.28, D.49, W.50, I.72, D.73, V.74, A.101, G.102, V.103, V.123 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.25, D:G.27, D:W.50, D:V.74, D:G.102 Water bridges: D:G.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Subramanian, V. et al., Phylogenetics-based identification and characterization of a superior 2,3-butanediol dehydrogenase for Zymomonas mobilis expression. Biotechnol Biofuels (2020)

Release Date

2020-12-23

Peptides

2,3-butanediol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2,3-butanediol dehydrogenase