SMTL ID : 7bu3.1

Structure of alcohol dehydrogenase YjgB in complex with NADP from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.1: 4 residues within 4Å: Chain A: M.313, S.314, K.335, A.336 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain A Hydrogen bonds: D.1, A:M.313, A:S.314, A:A.336

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 28 residues within 4Å: Chain A: C.40, H.41, S.42, W.51, C.151, T.155, G.175, I.176, G.177, G.178, L.179, S.198, S.199, N.200, K.203, T.237, V.238, N.239, V.240, V.260, G.261, A.262, S.284, A.285, T.286, R.331 Ligands: PEG.4, ZN.5 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.155 Hydrogen bonds: A:H.41, A:I.176, A:G.178, A:L.179, A:S.199, A:S.199, A:S.199, A:N.200, A:V.260, A:A.262, A:T.286 Water bridges: A:S.45, A:G.177, A:G.180, A:N.200, A:K.203, A:K.203, A:K.203, A:R.331 Salt bridges: A:H.41, A:K.203, A:R.331 NAP.7: 29 residues within 4Å: Chain B: C.39, H.40, S.41, W.50, C.150, T.154, G.174, I.175, G.176, G.177, L.178, S.197, S.198, N.199, K.202, R.218, T.236, V.237, N.238, V.239, V.259, G.260, A.261, S.283, A.284, T.285, R.330 Ligands: PEG.8, ZN.10 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:T.154, B:L.178 Hydrogen bonds: B:H.40, B:I.175, B:G.177, B:L.178, B:S.198, B:S.198, B:S.198, B:R.218, B:R.218, B:V.259, B:A.261, B:T.285 Water bridges: B:S.44, B:G.176, B:G.179, B:N.199, B:K.202, B:S.217, B:R.330 Salt bridges: B:H.40, B:K.202, B:R.330

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: S.198, S.199, N.200, P.201, E.204, V.215, N.217, R.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.199, A:E.204, A:R.219 Water bridges: A:N.217 GOL.9: 7 residues within 4Å: Chain B: S.197, S.198, N.199, P.200, E.203, V.214, N.216 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.203, B:N.216 Water bridges: B:N.216

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: W.51, W.90, A.285 Ligands: NAP.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.90, A:A.285 PEG.8: 3 residues within 4Å: Chain B: W.50, W.89 Ligands: NAP.7 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.89, B:A.284

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: C.40, H.62, E.63, C.151, R.331 Ligands: NAP.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.40, A:H.62, A:E.63, A:C.151 ZN.6: 6 residues within 4Å: Chain A: C.95, G.96, C.98, C.101, C.109, E.110 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.95, A:C.98, A:C.101, A:C.109 ZN.10: 5 residues within 4Å: Chain B: C.39, H.61, E.62, C.150 Ligands: NAP.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.39, B:H.61, B:E.62, B:C.150 ZN.11: 6 residues within 4Å: Chain B: C.94, G.95, C.97, C.100, C.108, E.109 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.94, B:C.97, B:C.100, B:C.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, G.T. et al., Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli . Molecules (2020)

Release Date

2020-05-13

Peptides

Alcohol dehydrogenase: A
Alcohol dehydrogenase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase

Alcohol dehydrogenase