SMTL ID : 4g74.1

Crystal structure of NDH with Quinone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

4 x UQ5: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE(Non-covalent)

UQ5.1: 6 residues within 4Å: Chain A: H.386, I.469, S.473, M.474, L.476 Ligands: UQ5.2 No protein-ligand interaction detected (PLIP) UQ5.2: 12 residues within 4Å: Chain A: W.52, P.81, A.382, Q.383, L.433, G.434, L.436, I.448, F.455, M.474 Ligands: UQ5.1, FAD.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.383, A:L.433, A:L.436, A:I.448, A:I.448, A:F.455 Water bridges: A:Q.383 UQ5.13: 12 residues within 4Å: Chain B: W.52, A.382, Q.383, H.386, L.433, G.434, L.436, I.448, Y.471, M.474 Ligands: UQ5.14, FAD.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.383, B:L.433, B:L.436 Hydrogen bonds: B:Y.471 UQ5.14: 7 residues within 4Å: Chain B: H.386, S.473, M.474, I.475, L.476, R.481 Ligands: UQ5.13 No protein-ligand interaction detected (PLIP)

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

TRT.3: 8 residues within 4Å: Chain A: L.482, F.486, I.489 Chain B: F.486, I.489, F.493, F.494 Ligands: TRT.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.482, A:I.489, B:I.489, B:F.494 TRT.4: 6 residues within 4Å: Chain A: I.489, F.493, F.494 Chain B: K.106, A.478 Ligands: TRT.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.489, A:F.494 pi-Stacking: A:F.493 TRT.5: 6 residues within 4Å: Chain A: R.468, L.472, F.485, W.488, I.489, A.492 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.472, A:F.485, A:W.488, A:W.488, A:A.492 TRT.15: 6 residues within 4Å: Chain B: R.468, I.469, L.472, F.485, W.488, A.492 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.468, B:I.469, B:L.472, B:W.488, B:A.492 Water bridges: B:R.468 pi-Cation interactions: B:R.468

11 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: K.246, L.491, F.494 No protein-ligand interaction detected (PLIP) MG.8: 8 residues within 4Å: Chain A: A.164, V.165, G.166, I.370, G.371, D.372, N.373 Ligands: FAD.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:I.370, FAD.7 MG.9: 7 residues within 4Å: Chain A: S.50, G.51, W.52, G.53, A.54, A.164 Ligands: FAD.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.164, FAD.7 MG.10: 4 residues within 4Å: Chain A: R.74, L.78, T.80 Ligands: FAD.7 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain A: G.166, A.167, K.185 Ligands: FAD.7 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: G.322 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.322, H2O.8, H2O.9, H2O.10 MG.16: 4 residues within 4Å: Chain B: D.243, L.491, F.494, R.496 No protein-ligand interaction detected (PLIP) MG.18: 8 residues within 4Å: Chain B: A.164, V.165, G.166, I.370, G.371, D.372, N.373 Ligands: FAD.17 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:I.370, FAD.17 MG.19: 6 residues within 4Å: Chain B: G.51, W.52, G.53, A.54, A.164 Ligands: FAD.17 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:A.164, FAD.17 MG.20: 6 residues within 4Å: Chain B: G.51, W.52, R.74, L.78, T.80 Ligands: FAD.17 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.78, H2O.8 MG.21: 5 residues within 4Å: Chain B: G.166, A.167, K.185, D.372 Ligands: FAD.17 No protein-ligand interaction detected (PLIP)

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

FAD.7: 33 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, 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: UQ5.2, MG.8, MG.9, MG.10, MG.11 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: 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:E.117, A:K.185, A:K.185, A:N.330, A:R.333, A:R.333, A:Q.383 FAD.17: 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, P.84, E.117, A.118, A.164, V.165, G.166, L.184, T.228, R.333, G.371, D.372, P.380, T.381, A.382, Q.383, A.385, Y.471 Ligands: UQ5.13, MG.18, MG.19, MG.20, MG.21 20 PLIP interactions: 20 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:D.372, B:P.380, B:A.382, B:Q.383, B:Y.471 Water bridges: B:R.74, B:R.74, B:K.185, B:A.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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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