SMTL ID : 4g73.1

Crystal structure of NDH with NADH and Quinone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

5 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: 3 residues within 4Å: Chain A: F.493, F.494 Chain B: L.482 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.493, A:F.493, A:F.494 UQ5.2: 2 residues within 4Å: Chain A: S.473, R.481 No protein-ligand interaction detected (PLIP) UQ5.4: 11 residues within 4Å: Chain A: W.52, A.382, Q.383, H.386, L.433, G.434, A.435, L.436, I.448, M.474 Ligands: FAD.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.433, A:L.436, A:I.448, A:I.448 UQ5.14: 3 residues within 4Å: Chain B: A.492, F.493, F.494 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.493, B:F.493, B:F.494, B:F.494 UQ5.15: 11 residues within 4Å: Chain B: W.52, A.382, Q.383, H.386, L.433, G.434, L.436, I.448, S.450, M.474 Ligands: FAD.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.433, B:L.436, B:I.448 Water bridges: B:Q.383

11 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: P.37, Q.38, S.40, K.42, N.44 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.42 MG.6: 8 residues within 4Å: Chain A: A.164, V.165, G.166, I.370, G.371, D.372, N.373 Ligands: FAD.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:I.370, FAD.5 MG.7: 6 residues within 4Å: Chain A: G.51, W.52, G.53, A.54, A.164 Ligands: FAD.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:A.164, FAD.5 MG.8: 7 residues within 4Å: Chain A: G.51, W.52, R.74, F.77, L.78, T.80 Ligands: FAD.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.78, H2O.1 MG.9: 5 residues within 4Å: Chain A: G.166, A.167, K.185, D.372 Ligands: FAD.5 No protein-ligand interaction detected (PLIP) MG.11: 1 residues within 4Å: Chain B: G.322 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.322, H2O.9 MG.12: 2 residues within 4Å: Chain B: L.105, K.107 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:L.105, B:K.107 MG.17: 8 residues within 4Å: Chain B: A.164, V.165, G.166, I.370, G.371, D.372, N.373 Ligands: FAD.16 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:I.370, FAD.16 MG.18: 6 residues within 4Å: Chain B: G.51, W.52, G.53, A.54, A.164 Ligands: FAD.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:A.164 MG.19: 7 residues within 4Å: Chain B: G.51, W.52, R.74, F.77, L.78, T.80 Ligands: FAD.16 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:L.78 MG.20: 5 residues within 4Å: Chain B: G.166, A.167, K.185, D.372 Ligands: FAD.16 No protein-ligand interaction detected (PLIP)

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

FAD.5: 36 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, L.83, 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: UQ5.4, MG.6, MG.7, MG.8, MG.9, NAI.10 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:L.83, 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:G.166, 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:R.333, A:A.385, A:Y.471 Salt bridges: A:K.185 FAD.16: 36 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, K.185, T.228, R.333, I.370, G.371, D.372, P.380, T.381, A.382, Q.383, A.385, Y.471 Ligands: NAI.13, UQ5.15, MG.17, MG.18, MG.19, MG.20 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:K.185, 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:G.166, 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:Q.383, B:A.385 Salt bridges: B:K.185

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.10: 22 residues within 4Å: Chain A: F.172, V.223, G.224, G.225, G.226, P.227, T.228, E.231, V.260, E.261, A.262, L.263, T.293, A.294, V.295, A.327, T.328, G.329, P.380, L.436, Y.471 Ligands: FAD.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.227 Hydrogen bonds: A:G.225, A:G.226, A:T.228, A:T.228, A:E.231, A:A.262, A:L.263, A:V.295, A:V.295, A:T.328, A:G.329, A:L.436 Water bridges: A:G.226, A:A.327, A:Y.471 NAI.13: 22 residues within 4Å: Chain B: V.223, G.224, G.225, G.226, P.227, T.228, E.231, V.260, E.261, A.262, L.263, T.293, A.294, V.295, A.327, T.328, G.329, P.380, T.381, L.436, Y.471 Ligands: FAD.16 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.227 Hydrogen bonds: B:G.225, B:A.262, B:V.295, B:V.295, B:T.328, B:G.329, B:L.436, B:L.436, B:Y.471 Water bridges: B:G.225, B:G.226, B:T.228, B:E.261

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

Related Entries With Identical Sequence