SMTL ID : 5kms.1 (1 other biounit)

The structure of type II NADH dehydrogenase from Caldalkalibacillus thermarum complexed with NAD+ at 2.5 angstrom resolution.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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, Y.43, T.45, T.46, H.49, D.79, T.80, V.81, G.106, L.107, G.108, I.126, T.166, E.169, N.265, I.267, G.298, D.299, P.314, T.315, A.316, Q.317, A.319, K.376 Ligands: NAD.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:H.49 Hydrogen bonds: A:A.11, A:A.11, A:G.12, A:Y.13, A:G.14, A:N.37, A:K.38, A:N.39, A:Y.43, A:T.45, A:T.45, A:V.81, A:V.81, A:G.108, A:N.265, A:D.299, A:P.314, A:A.316, A:Q.317, A:K.376 Water bridges: A:Q.317, A:T.349, A:K.376 FAD.3: 32 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, H.49, D.79, T.80, V.81, G.106, L.107, G.108, I.126, F.165, T.166, E.169, N.265, I.267, G.298, D.299, P.314, T.315, A.316, Q.317, A.319, T.349, K.376 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:H.49, 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: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:A.316, B:Q.317, B:K.376 Water bridges: B:G.12, B:G.12, B:Y.43, B:S.109, B:S.109, B:C.300

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

NAD.2: 24 residues within 4Å: Chain A: F.114, I.116, G.162, G.164, F.165, T.166, E.169, V.197, E.198, A.199, P.205, T.230, P.231, I.232, W.258, T.259, G.260, G.261, V.262, P.313, P.314, T.349, V.350 Ligands: FAD.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.165 Hydrogen bonds: A:T.166, A:T.166, A:A.199, A:I.232, A:I.232, A:T.259, A:T.349, A:V.350 Water bridges: A:G.164, A:T.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaza, J.N. et al., The mechanism of catalysis by type-II NADH:quinone oxidoreductases. Sci Rep (2017)

Release Date

2017-02-01

Peptides

FAD-dependent pyridine nucleotide-disulfide oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FAD-dependent pyridine nucleotide-disulfide oxidoreductase

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