SMTL ID : 6sch.1

NADH-dependent variant of CBADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 28 residues within 4Å: Chain A: C.37, T.38, S.39, H.42, H.59, D.150, M.151, T.154, I.173, G.174, G.176, A.177, V.178, V.197, D.198, Y.199, R.200, A.242, G.243, G.244, E.247, I.265, N.266, Y.267, L.294, K.340 Ligands: ZN.5, MG.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.154, A:V.178 Hydrogen bonds: A:T.38, A:S.39, A:S.39, A:H.42, A:V.178, A:Y.199, A:E.247, A:Y.267 Water bridges: A:T.38, A:C.295 Salt bridges: A:K.340 NAD.8: 26 residues within 4Å: Chain A: M.285 Chain B: T.38, S.39, H.42, H.59, D.150, T.154, I.173, G.174, G.176, A.177, V.178, V.197, D.198, Y.199, R.200, A.242, G.243, G.244, E.247, T.248, I.265, N.266, Y.267, L.294 Ligands: ZN.11 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.154, B:V.178 Hydrogen bonds: B:T.38, B:T.38, B:S.39, B:G.174, B:V.178, B:Y.199, B:R.200, B:E.247, B:E.247, B:Y.267 Water bridges: B:G.176, B:G.179, B:Q.251, B:Q.251, B:C.295 Salt bridges: B:R.200, B:K.340 NAD.12: 24 residues within 4Å: Chain C: T.38, S.39, W.110, D.150, T.154, I.173, G.174, G.176, A.177, V.178, V.197, D.198, Y.199, R.200, P.218, A.242, G.243, G.244, E.247, I.265, N.266, Y.267, K.340 Ligands: ZN.14 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.154, C:V.178 Hydrogen bonds: C:T.38, C:S.39, C:S.39, C:V.178, C:E.247, C:Y.267 Water bridges: C:T.38, C:G.179 Salt bridges: C:R.200, C:K.340 pi-Stacking: C:Y.199 NAD.15: 26 residues within 4Å: Chain C: M.285 Chain D: T.38, S.39, H.42, H.59, W.110, D.150, T.154, I.173, G.174, G.176, A.177, V.178, V.197, D.198, Y.199, R.200, A.242, G.243, G.244, E.247, I.265, N.266, Y.267, K.340 Ligands: ZN.18 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:T.154, D:V.178 Hydrogen bonds: D:T.38, D:H.42, D:A.177, D:V.178, D:Y.199, D:E.247, D:E.247, D:N.266, D:Y.267

8 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.2: 8 residues within 4Å: Chain A: S.317, K.318, V.320, T.321, H.322, V.323, D.343 Ligands: MG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.321 2PE.3: 13 residues within 4Å: Chain A: Q.165, S.169, K.234, G.235, D.237, R.238, K.257, P.258, G.259, G.260 Chain B: L.93, E.94, A.97 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.169, A:S.169, A:R.238, A:K.257 Water bridges: A:Q.165, A:R.238 2PE.4: 8 residues within 4Å: Chain A: Y.25, D.89, R.91, N.104 Chain C: Y.25, D.89, R.91, N.104 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.91, A:D.89, A:R.91, A:N.104 Water bridges: C:N.104 2PE.9: 12 residues within 4Å: Chain A: L.93, E.94, A.97, F.99 Chain B: S.169, K.234, G.235, D.237, R.238, K.257, P.258, G.259 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.169, B:S.169, B:D.237, B:R.238, B:K.257 2PE.10: 9 residues within 4Å: Chain B: Y.25, D.89, R.91, N.104, D.128 Chain D: Y.25, D.89, R.91, D.128 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:D.89, B:R.91, B:N.104, D:R.91 2PE.13: 12 residues within 4Å: Chain C: Q.165, S.169, K.234, G.235, D.237, R.238, K.257, P.258, G.259 Chain D: L.93, A.97, F.99 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.169, C:S.169, C:R.238, C:R.238, C:K.257 2PE.16: 10 residues within 4Å: Chain C: A.97, F.99 Chain D: Q.165, S.169, K.234, G.235, D.237, R.238, K.257, P.258 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.169, D:S.169, D:D.237, D:R.238, D:R.238, D:K.257 2PE.17: 3 residues within 4Å: Chain D: E.18, R.19, Y.123 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.19

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: C.37, S.39, H.59, D.150 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.37, A:H.59, A:D.150 ZN.11: 6 residues within 4Å: Chain B: C.37, S.39, H.59, E.60, D.150 Ligands: NAD.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.37, B:H.59, B:D.150 ZN.14: 6 residues within 4Å: Chain C: C.37, S.39, H.59, E.60, D.150 Ligands: NAD.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.37, C:H.59, C:D.150 ZN.18: 5 residues within 4Å: Chain D: C.37, S.39, H.59, D.150 Ligands: NAD.15 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.37, D:H.59, D:D.150

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: V.320 Ligands: 2PE.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: G.243, G.244 Ligands: NAD.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selles Vidal, L. et al., Versatile selective evolutionary pressure using synthetic defect in universal metabolism. Nat Commun (2021)

Release Date

2020-08-26

Peptides

NADP-dependent isopropanol dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NADP-dependent isopropanol dehydrogenase