SMTL ID : 6xex.1

Structure of Serratia marcescens 2,3-butanediol dehydrogenase mutant Q247A/V139Q

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 30 residues within 4Å: Chain A: G.25, G.27, 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: EDO.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:P.194 Hydrogen bonds: A:G.25, A:G.27, A:N.28, 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:V.197, A:T.199, A:N.200, A:M.201 Water bridges: A:G.31, A:N.100, A:N.200, A:N.200 pi-Stacking: A:W.50, A:W.50 NAD.9: 30 residues within 4Å: Chain C: G.25, G.27, 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: EDO.12 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:P.194 Hydrogen bonds: C:G.25, C:G.27, C:N.28, 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:V.197, C:T.199, C:T.199, C:N.200, C:M.201 Water bridges: C:G.31, C:N.100, C:N.200, C:N.200 pi-Stacking: C:W.50, C:W.50

4 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: N.200, N.203, G.204 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.200, A:G.204 NA.7: 5 residues within 4Å: Chain B: S.195, L.196, I.217, A.222, A.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.195, B:A.223 NA.10: 3 residues within 4Å: Chain C: N.200, N.203, G.204 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.203, C:G.204 NA.15: 5 residues within 4Å: Chain D: S.195, L.196, I.217, A.222, A.223 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.196, D:A.223

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: W.117, R.118, A.121, D.126 Chain D: W.117, R.118, A.121, D.126 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:R.118, D:R.118, D:D.126, A:R.118, A:R.118, A:D.126 EDO.4: 6 residues within 4Å: Chain A: S.151, Q.152, S.153, Y.164, W.205 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.151, A:S.153, A:Y.164, A:Y.164 EDO.5: 4 residues within 4Å: Chain A: K.198, T.199, N.200, N.203 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.199, A:N.203 EDO.6: 5 residues within 4Å: Chain A: W.50, D.73, S.75, R.118, R.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.73, A:S.75, A:R.118 EDO.8: 4 residues within 4Å: Chain B: K.52, D.56, A.69, H.71 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.52, B:D.56 EDO.11: 8 residues within 4Å: Chain B: W.117, R.118, A.121, D.126 Chain C: W.117, R.118, A.121, D.126 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.118, B:R.118, B:D.126, C:R.118, C:R.118, C:D.126 EDO.12: 6 residues within 4Å: Chain C: S.151, Q.152, S.153, Y.164, W.205 Ligands: NAD.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.151, C:S.153, C:Y.164 EDO.13: 4 residues within 4Å: Chain C: K.198, T.199, N.200, N.203 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.199, C:N.203 EDO.14: 5 residues within 4Å: Chain C: W.50, D.73, S.75, R.118, R.119 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.73, C:S.75, C:R.118 Water bridges: C:D.73 EDO.16: 4 residues within 4Å: Chain D: K.52, D.56, A.69, H.71 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.52, D:D.56

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