SMTL ID : 7bu2.1

Structure of alcohol dehydrogenase YjgB from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 6 residues within 4Å: Chain A: S.74, A.75, A.76, Q.77, D.78, K.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.77, A:D.78, A:K.79 NO3.8: 5 residues within 4Å: Chain B: S.315, K.316, I.317, N.318, D.319 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.316, B:K.316, B:N.318, B:N.318, B:D.319

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.3: 3 residues within 4Å: Chain A: T.169, R.171, E.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.194 GOL.4: 5 residues within 4Å: Chain A: G.105, N.106, T.289, Y.291, E.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.106, A:T.289, A:E.292 GOL.5: 3 residues within 4Å: Chain A: I.276, A.277, D.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.277 GOL.9: 4 residues within 4Å: Chain B: I.276, A.277, G.278, D.279 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.277, B:D.279 GOL.10: 5 residues within 4Å: Chain B: S.43, W.91, C.152, A.286, T.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.43 Water bridges: B:S.43

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: C.41, H.63, E.64, C.152, R.332 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.41, A:H.63, A:E.64, A:C.152 ZN.7: 6 residues within 4Å: Chain A: C.96, G.97, C.99, C.102, C.110, E.111 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.96, A:C.99, A:C.102, A:C.110 ZN.11: 7 residues within 4Å: Chain B: C.96, G.97, C.99, C.102, C.110, E.111, Q.112 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.96, B:C.99, B:C.102, B:C.110 ZN.12: 5 residues within 4Å: Chain B: C.41, H.63, E.64, C.152, R.332 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.41, B:H.63, B:E.64, B:C.152, H2O.15

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase