SMTL ID : 4gkv.1

Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-4-1-mer

Ligands

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

NAD.1: 31 residues within 4Å: Chain A: C.37, H.38, T.39, H.42, C.145, T.149, G.169, L.170, G.171, G.172, L.173, I.192, D.193, V.194, Q.198, S.213, T.235, A.236, V.237, A.238, A.241, V.258, G.259, L.260, S.282, L.283, V.284, M.321, R.329 Chain D: V.273 Ligands: ZN.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.149, A:L.173 Hydrogen bonds: A:H.38, A:H.38, A:L.170, A:G.172, A:L.173, A:Q.198, A:S.213, A:V.237, A:V.258, A:L.260, A:V.284, A:R.329 Water bridges: A:G.171, A:G.174, A:N.195, A:N.195, A:S.213, A:S.213 Salt bridges: A:H.38, A:H.38, A:R.329 NAD.4: 32 residues within 4Å: Chain B: C.37, H.38, T.39, H.42, C.145, T.149, G.169, L.170, G.171, G.172, L.173, I.192, D.193, V.194, N.195, Q.198, S.213, T.235, A.236, V.237, A.238, A.241, V.258, G.259, L.260, S.282, L.283, V.284, M.321, R.329 Chain C: V.273 Ligands: ZN.5 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:T.149, B:L.173, B:L.173, B:V.258 Hydrogen bonds: B:H.38, B:T.39, B:H.42, B:T.149, B:L.170, B:G.172, B:L.173, B:Q.198, B:S.213, B:V.237, B:V.258, B:L.260, B:V.284, B:R.329 Water bridges: B:G.171, B:G.174, B:N.195, B:S.213, B:S.213 Salt bridges: B:H.38, B:R.329 NAD.8: 30 residues within 4Å: Chain B: V.273 Chain C: C.37, H.38, T.39, H.42, C.145, T.149, G.169, L.170, G.171, G.172, L.173, D.193, V.194, Q.198, S.213, T.235, A.236, V.237, A.238, A.241, V.258, G.259, L.260, S.282, L.283, V.284, M.321, R.329 Ligands: ZN.9 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:T.149, C:L.173 Hydrogen bonds: C:H.38, C:H.42, C:T.149, C:L.170, C:G.172, C:L.173, C:V.194, C:Q.198, C:S.213, C:V.237, C:V.258, C:L.260, C:V.284, C:R.329 Water bridges: C:G.171, C:G.174, C:S.213 Salt bridges: C:H.38, C:H.38, C:R.329 NAD.12: 32 residues within 4Å: Chain A: V.273 Chain D: C.37, H.38, T.39, H.42, C.145, T.149, G.169, L.170, G.171, G.172, L.173, I.192, D.193, V.194, N.195, Q.198, S.213, T.235, A.236, V.237, A.238, A.241, V.258, G.259, L.260, S.282, L.283, V.284, M.321, R.329 Ligands: ZN.13 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:T.149, D:L.173 Hydrogen bonds: D:H.38, D:H.42, D:L.170, D:G.172, D:L.173, D:V.194, D:Q.198, D:S.213, D:V.237, D:V.258, D:L.260, D:V.284, D:R.329 Water bridges: D:G.171, D:G.174, D:N.195, D:S.213, D:S.213 Salt bridges: D:H.38, D:H.38, D:R.329

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.37, T.39, H.58, C.145 Ligands: NAD.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.37, A:H.58, A:C.145, H2O.1 ZN.3: 5 residues within 4Å: Chain A: C.89, G.90, C.92, C.95, C.103 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.89, A:C.92, A:C.95, A:C.103 ZN.5: 5 residues within 4Å: Chain B: C.37, T.39, H.58, C.145 Ligands: NAD.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.37, B:H.58, B:C.145, H2O.33 ZN.6: 5 residues within 4Å: Chain B: C.89, G.90, C.92, C.95, C.103 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.89, B:C.92, B:C.95, B:C.103 ZN.9: 5 residues within 4Å: Chain C: C.37, T.39, H.58, C.145 Ligands: NAD.8 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.37, C:H.58, C:C.145, H2O.49 ZN.10: 5 residues within 4Å: Chain C: C.89, G.90, C.92, C.95, C.103 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.89, C:C.92, C:C.95, C:C.103 ZN.13: 5 residues within 4Å: Chain D: C.37, T.39, H.58, C.145 Ligands: NAD.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.37, D:H.58, D:C.145, H2O.51 ZN.14: 5 residues within 4Å: Chain D: C.89, G.90, C.92, C.95, C.103 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.89, D:C.92, D:C.95, D:C.103

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain B: H.38, H.42, N.45, D.47 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.38, B:N.45, B:D.47 Water bridges: B:D.47 GOL.11: 6 residues within 4Å: Chain C: H.38, L.41, H.42, N.45, D.47, P.262 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.38, C:N.45, C:D.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomas, L.M. et al., Structure of Escherichia coli AdhP (ethanol-inducible dehydrogenase) with bound NAD. Acta Crystallogr.,Sect.F (2013)

Release Date

2013-07-10

Peptides

Alcohol dehydrogenase, propanol-preferring: ABCD
cleaved peptide fragment corresponding to the C-terminal His tag: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
P

Alcohol dehydrogenase, propanol-preferring

cleaved peptide fragment corresponding to the C-terminal His tag