SMTL ID : 5er0.1 (1 other biounit)

Water-forming NADH oxidase from Lactobacillus brevis (LbNOX)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: G.57, C.58, T.59, H.60, A.61, Y.81, E.82, R.83, N.84, S.91, C.92, H.127, N.128, V.129, T.160, S.161, G.162, S.163, C.181, K.182, Y.207, I.208, F.292, N.295, L.298, G.328, D.329, P.345, L.346, A.347, T.348, A.350 Chain B: F.472, Q.473 Ligands: OXY.2, EDO.5 36 PLIP interactions: 33 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.208, A:I.208, A:F.292 Hydrogen bonds: A:C.58, A:T.59, A:T.59, A:T.59, A:T.59, A:H.60, A:A.61, A:R.83, A:R.83, A:N.84, A:V.129, A:V.129, A:S.163, A:D.329, A:P.345, A:A.347, A:T.348, B:F.472 Water bridges: A:H.60, A:N.84, A:N.84, A:N.84, A:N.84, A:S.91, A:S.91, A:S.91, A:N.295, A:S.330, A:L.346, B:F.472, B:Q.473 Salt bridges: A:K.182 pi-Stacking: A:Y.207 FAD.7: 35 residues within 4Å: Chain A: F.472, Q.473 Chain B: G.57, C.58, T.59, H.60, A.61, Y.81, E.82, R.83, N.84, S.91, C.92, H.127, N.128, V.129, T.160, S.161, G.162, S.163, C.181, K.182, Y.207, I.208, F.292, N.295, L.298, G.328, D.329, P.345, L.346, A.347, T.348, A.350 Ligands: OXY.8 38 PLIP interactions: 35 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.208, B:I.208, B:F.292 Hydrogen bonds: B:C.58, B:T.59, B:T.59, B:T.59, B:T.59, B:H.60, B:A.61, B:R.83, B:R.83, B:N.84, B:V.129, B:V.129, B:S.163, B:D.329, B:P.345, B:A.347, B:T.348, A:F.472 Water bridges: B:H.60, B:G.62, B:N.84, B:N.84, B:N.84, B:N.84, B:S.91, B:S.91, B:S.91, B:N.128, B:N.183, B:N.295, B:D.329, A:F.472, A:Q.473 Salt bridges: B:K.182 pi-Stacking: B:Y.207

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.2: 6 residues within 4Å: Chain A: H.60, L.90, S.91, C.92 Chain B: F.472 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.91, A:C.92 OXY.8: 5 residues within 4Å: Chain A: F.472 Chain B: L.90, S.91, C.92 Ligands: FAD.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.91, B:C.92

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: V.86, I.87, Q.106, F.109, S.111, S.112, P.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.87, A:I.87, A:Q.106 Water bridges: A:Q.106 EDO.4: 4 residues within 4Å: Chain A: F.64, Y.110 Chain B: R.478, P.479 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.478, B:R.478, B:R.478 EDO.5: 7 residues within 4Å: Chain A: Y.207, Y.236, L.346, S.375, G.376 Chain B: F.472 Ligands: FAD.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.236, A:S.375, A:G.376, A:G.376 Water bridges: B:F.472 EDO.6: 4 residues within 4Å: Chain A: R.382, E.407, M.440, S.441 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.382, A:M.440 Water bridges: A:K.442 EDO.9: 4 residues within 4Å: Chain A: R.478, P.479 Chain B: F.64, Y.110 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.478 EDO.10: 8 residues within 4Å: Chain B: R.199, I.200, T.201, D.222, V.223, T.224, E.282, T.283 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.223, B:E.282 EDO.11: 5 residues within 4Å: Chain B: R.382, E.407, M.440, S.441, K.442 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.382, B:E.407, B:K.442

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Titov, D.V. et al., Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio. Science (2016)

Release Date

2016-04-13

Peptides

NADH oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NADH oxidase

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