SMTL ID : 4g6g.1

Crystal structure of NDH with TRT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

6 x TRT: FRAGMENT OF TRITON X-100(Non-covalent)

TRT.1: 5 residues within 4Å: Chain A: R.468, I.469, F.485, W.488, A.492 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.468, A:I.469, A:I.469, A:F.485, A:W.488 Water bridges: A:R.468 pi-Cation interactions: A:R.468 TRT.2: 12 residues within 4Å: Chain A: W.52, A.382, Q.383, H.386, L.433, G.434, A.435, L.436, I.448, L.470, M.474 Ligands: FAD.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.383, A:L.433, A:L.433, A:I.448 TRT.8: 7 residues within 4Å: Chain A: A.478, L.482, F.486 Chain B: I.489, F.493, F.494 Ligands: TRT.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.482, A:F.486, B:I.489, B:F.493 TRT.9: 6 residues within 4Å: Chain A: F.493, F.494 Chain B: K.106, A.478, L.482 Ligands: TRT.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.493, A:F.494, B:A.478 TRT.10: 5 residues within 4Å: Chain B: R.468, I.469, F.485, W.488, A.492 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.485, B:W.488 Water bridges: B:R.468 pi-Cation interactions: B:R.468 TRT.11: 10 residues within 4Å: Chain B: W.52, Q.383, H.386, L.433, G.434, A.435, L.436, I.448, M.474 Ligands: FAD.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.383, B:I.448

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

FAD.3: 34 residues within 4Å: Chain A: G.49, S.50, G.51, W.52, G.53, I.71, S.72, P.73, R.74, T.80, P.81, P.84, E.117, A.118, A.164, V.165, G.166, L.184, K.185, T.228, R.333, G.371, D.372, P.380, T.381, A.382, Q.383, A.385, Y.471 Ligands: TRT.2, MG.4, MG.5, MG.6, MG.7 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.84, A:K.185, A:T.228 Hydrogen bonds: A:S.50, A:S.50, A:W.52, A:G.53, A:S.72, A:R.74, A:T.80, A:A.118, A:A.118, A:D.372, A:P.380, A:A.382, A:Q.383 Water bridges: A:R.74, A:R.74, A:R.74, A:R.74, A:E.117, A:K.185, A:K.185, A:A.385, A:Y.471 Salt bridges: A:K.185 FAD.14: 33 residues within 4Å: Chain B: G.49, S.50, G.51, W.52, G.53, I.71, S.72, P.73, R.74, T.80, P.81, E.117, A.118, A.164, V.165, G.166, L.184, K.185, T.228, R.333, G.371, D.372, P.380, T.381, A.382, Q.383, A.385, Y.471 Ligands: TRT.11, MG.15, MG.16, MG.17, MG.18 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:T.228 Hydrogen bonds: B:S.50, B:S.50, B:W.52, B:G.53, B:S.72, B:R.74, B:T.80, B:T.80, B:A.118, B:A.118, B:I.370, B:D.372, B:P.380, B:A.382, B:Q.383 Water bridges: B:R.74, B:R.74, B:K.185, B:K.185, B:K.185, B:A.385 Salt bridges: B:K.185

10 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 8 residues within 4Å: Chain A: A.164, V.165, G.166, I.370, G.371, D.372, N.373 Ligands: FAD.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:I.370, FAD.3 MG.5: 6 residues within 4Å: Chain A: G.51, W.52, G.53, A.54, A.164 Ligands: FAD.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.164, FAD.3 MG.6: 7 residues within 4Å: Chain A: G.51, W.52, R.74, F.77, L.78, T.80 Ligands: FAD.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.78, H2O.1 MG.7: 5 residues within 4Å: Chain A: G.166, A.167, K.185, D.372 Ligands: FAD.3 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: G.322 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.322, H2O.11, H2O.13, H2O.14, H2O.15 MG.13: 2 residues within 4Å: Chain B: L.105, K.107 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.105, B:K.107, H2O.11 MG.15: 8 residues within 4Å: Chain B: A.164, V.165, G.166, I.370, G.371, D.372, N.373 Ligands: FAD.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:I.370, FAD.14 MG.16: 6 residues within 4Å: Chain B: G.51, W.52, G.53, A.54, A.164 Ligands: FAD.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.164 MG.17: 6 residues within 4Å: Chain B: G.51, W.52, R.74, L.78, T.80 Ligands: FAD.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.78, H2O.11 MG.18: 5 residues within 4Å: Chain B: G.166, A.167, K.185, D.372 Ligands: FAD.14 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.372

Links

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Citation

Feng, Y. et al., Structural insight into the type-II mitochondrial NADH dehydrogenases. Nature (2012)

Release Date

2012-10-24

Peptides

Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial

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