SMTL ID : 6bdo.2 (1 other biounit)

Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with a quinone inhibitor HQNO at 2.8A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 31 residues within 4Å: Chain A: G.10, A.11, G.12, Y.13, G.14, N.37, K.38, N.39, Y.43, T.45, T.46, H.49, D.79, T.80, V.81, G.106, L.107, G.108, I.126, F.165, T.166, N.265, I.267, G.298, D.299, P.314, T.315, A.316, Q.317, A.319, K.376 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:T.45, A:H.49, A:T.166 Hydrogen bonds: A:A.11, A:Y.13, A:G.14, A:N.37, A:K.38, A:N.39, A:T.45, A:V.81, A:V.81, A:S.109, A:N.265, A:D.299, A:P.314, A:A.316, A:Q.317, A:K.376 FAD.2: 31 residues within 4Å: Chain B: G.10, A.11, G.12, Y.13, G.14, N.37, K.38, Y.43, T.45, T.46, D.79, T.80, V.81, G.106, L.107, G.108, I.126, F.165, T.166, N.265, I.267, G.298, D.299, P.314, T.315, A.316, Q.317, A.319, T.349, K.376 Ligands: HQO.3 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:T.45, B:T.166 Hydrogen bonds: B:A.11, B:A.11, B:Y.13, B:G.14, B:N.37, B:K.38, B:N.39, B:Y.43, B:T.45, B:T.45, B:V.81, B:V.81, B:G.108, B:N.265, B:D.299, B:P.314, B:T.315, B:A.316, B:Q.317, B:T.349, B:T.349, B:K.376 Water bridges: B:Y.43, B:Y.43, B:N.127

1 x HQO: 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE(Non-covalent)

HQO.3: 10 residues within 4Å: Chain B: A.316, Q.317, I.320, R.347, G.348, T.349, I.379, R.382, Y.383 Ligands: FAD.2 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.316, B:Q.317, B:I.320, B:R.347, B:I.379, B:I.379, B:I.379, B:Y.383 Hydrogen bonds: B:Q.317, B:T.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Petri, J. et al., Structure of the NDH-2 - HQNO inhibited complex provides molecular insight into quinone-binding site inhibitors. Biochim. Biophys. Acta (2018)

Release Date

2018-05-16

Peptides

FAD-dependent pyridine nucleotide-disulfide oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

FAD-dependent pyridine nucleotide-disulfide oxidoreductase

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