SMTL ID : 6qti.1

Structure of ovine transhydrogenase in the presence of NADP+ in a "double face-down" conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 26 residues within 4Å: Chain A: A.829, D.830, P.832, M.876, M.880, G.932, Y.933, G.934, A.938, V.965, A.966, G.967, R.968, M.969, G.1007, A.1008, N.1009, D.1010, T.1011, M.1041, K.1042, R.1043, S.1044, G.1048, D.1068, A.1069 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.832, A:P.832, A:V.965 Hydrogen bonds: A:Y.933, A:A.966, A:R.968, A:M.969, A:N.1009, A:N.1009, A:D.1010, A:T.1011, A:K.1042, A:R.1043, A:S.1044, A:S.1044, A:D.1068, A:A.1069 Salt bridges: A:K.1042, A:R.1043 pi-Cation interactions: A:R.1043 NAP.11: 24 residues within 4Å: Chain B: A.829, D.830, P.832, M.876, M.880, G.934, A.938, V.965, A.966, G.967, R.968, G.1007, A.1008, N.1009, D.1010, T.1011, K.1042, R.1043, S.1044, V.1047, G.1048, Y.1049, D.1068, A.1069 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:P.832, B:P.832, B:V.965 Hydrogen bonds: B:V.965, B:R.968, B:N.1009, B:D.1010, B:D.1010, B:T.1011, B:R.1043, B:S.1044, B:S.1044, B:Y.1049, B:D.1068, B:A.1069 Salt bridges: B:K.1042, B:R.1043 pi-Cation interactions: B:R.1043, B:R.1043

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

NAD.2: 16 residues within 4Å: Chain A: R.182, G.234, G.235, G.236, V.237, D.257, T.258, R.259, G.287, Y.288, A.289, E.300, T.317, A.318, L.319, I.320 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.182, A:G.235, A:V.237, A:R.259, A:R.259, A:G.287, A:E.300, A:L.319, A:L.319 Salt bridges: A:R.182 NAD.12: 19 residues within 4Å: Chain B: R.182, Q.187, D.190, S.193, G.234, G.235, G.236, V.237, D.257, T.258, R.259, G.287, A.289, E.300, T.317, A.318, L.319, I.320, P.326 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.182, B:Q.187, B:G.235, B:V.237, B:D.257, B:R.259, B:R.259, B:R.259, B:R.259, B:E.300, B:L.319, B:L.319 Salt bridges: B:R.182

12 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.3: 9 residues within 4Å: Chain A: G.509, Y.513, W.517, W.844, S.867, A.870, Y.874 Ligands: PC1.4, PC1.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.844, A:A.870, A:Y.874 pi-Cation interactions: A:W.517, A:W.517 PC1.4: 17 residues within 4Å: Chain A: Y.479, G.482, I.486, L.489, F.505, G.506, Y.513, H.514 Chain B: G.518, L.629, V.632, G.633, A.636, S.639 Ligands: PC1.3, D12.6, PC1.10 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.479, A:L.489, A:F.505, A:Y.513 Salt bridges: A:H.514 Hydrogen bonds: B:S.639 PC1.5: 12 residues within 4Å: Chain A: Y.841, W.844, C.847, S.873, Y.874, C.877, V.878, R.882, S.883, L.884 Ligands: PC1.3, D12.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.844, A:W.844 PC1.7: 15 residues within 4Å: Chain A: F.575, L.576, Q.579, D.583, N.595, Y.598, L.599, A.602, G.603, A.649, M.652, I.653, V.655, A.656, L.688 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.575, A:L.576, A:N.595, A:A.649, A:M.652, A:I.653, A:V.655, A:A.656, A:L.688 Hydrogen bonds: A:Q.579, A:D.583 PC1.8: 6 residues within 4Å: Chain A: L.610, A.611, L.613, Y.614, L.663, P.668 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.610, A:A.611, A:L.613, A:Y.614, A:L.663, A:L.663 PC1.9: 14 residues within 4Å: Chain A: L.629, C.630, G.633, A.636 Chain B: Y.479, L.483, L.489, V.502, G.506, I.510, Y.513, H.514 Ligands: PC1.13, PC1.15 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.479, B:L.483, B:L.489, B:V.502, B:Y.513, B:Y.513, A:L.629 Hydrogen bonds: B:Y.513 Salt bridges: B:H.514, B:H.514 PC1.10: 8 residues within 4Å: Chain A: G.488, L.489, I.491, A.492 Chain B: S.612, S.615, Y.617 Ligands: PC1.4 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.615, B:Y.617 Hydrophobic interactions: A:L.489, A:A.492 PC1.13: 11 residues within 4Å: Chain B: F.505, G.509, Y.513, W.517, S.867, A.870, I.871, Y.874 Ligands: PC1.9, PC1.14, PC1.15 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.505, B:A.870, B:Y.874 Hydrogen bonds: B:Y.513 pi-Cation interactions: B:W.517 PC1.14: 14 residues within 4Å: Chain B: S.840, Y.841, W.844, A.848, F.851, A.870, S.873, Y.874, V.878, R.882, S.883, L.884 Ligands: PC1.13, D12.16 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.841, B:W.844, B:A.848, B:F.851, B:F.851, B:A.870, B:Y.874, B:L.884 Hydrogen bonds: B:Y.874 PC1.15: 10 residues within 4Å: Chain A: T.643 Chain B: V.478, Y.479, A.481, G.482, G.485, L.489 Ligands: PC1.9, PC1.13, D12.17 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.478, B:Y.479, B:L.489 Hydrogen bonds: B:Y.479 PC1.18: 15 residues within 4Å: Chain B: F.575, L.576, Q.579, D.583, N.595, Y.598, L.599, A.602, G.603, V.606, A.649, M.652, I.653, A.656, L.688 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.575, B:F.575, B:L.576, B:L.599, B:V.606, B:A.649, B:M.652, B:I.653, B:A.656, B:L.688 Hydrogen bonds: B:Q.579, B:N.595 PC1.19: 6 residues within 4Å: Chain B: L.610, L.613, Y.614, L.663, K.667, P.668 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.610, B:L.613, B:L.663

3 x D12: DODECANE(Non-covalent)

D12.6: 9 residues within 4Å: Chain A: L.489, A.492, F.498, F.505, L.737, V.741, F.851 Ligands: PC1.4, PC1.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.489, A:L.489, A:A.492, A:F.498, A:F.498, A:F.505, A:L.737, A:V.741, A:F.851 D12.16: 6 residues within 4Å: Chain B: A.492, F.498, L.737, F.851 Ligands: PC1.14, D12.17 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.492, B:F.498, B:L.737, B:F.851, B:F.851 D12.17: 5 residues within 4Å: Chain B: G.488, L.489, A.492 Ligands: PC1.15, D12.16 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.489, B:A.492

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kampjut, D. et al., Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature (2019)

Release Date

2019-08-28

Peptides

Nicotinamide nucleotide transhydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Nicotinamide nucleotide transhydrogenase

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