SMTL ID : 6l7o.1

cryo-EM structure of cyanobacteria Fd-NDH-1L complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

3 x BCR: BETA-CAROTENE(Covalent)

BCR.1: 12 residues within 4Å: Chain A: T.312, Y.319, F.320, F.323, L.324 Chain I: L.25, F.29 Chain L: F.42, A.45, F.46, F.49 Ligands: DGD.4 9 PLIP interactions: 3 interactions with chain A, 5 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: A:T.312, A:F.320, A:F.320, L:F.42, L:A.45, L:F.46, L:F.46, L:F.49, I:F.29 BCR.44: 11 residues within 4Å: Chain D: I.290, L.294, F.421, V.425 Chain F: F.187, I.231, L.235, P.245, L.597 Chain Q: F.31 Ligands: SQD.48 8 PLIP interactions: 4 interactions with chain F, 3 interactions with chain D, 1 interactions with chain Q Hydrophobic interactions: F:F.187, F:I.231, F:P.245, F:L.597, D:F.421, D:F.421, D:V.425, Q:F.31 BCR.74: 13 residues within 4Å: Chain D: L.471, V.472, P.473, I.475, G.476, I.477 Chain F: L.20, I.27 Chain P: I.10, M.14 Ligands: LHG.30, LHG.46, SQD.47 10 PLIP interactions: 2 interactions with chain P, 6 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: P:I.10, P:M.14, D:L.471, D:V.472, D:P.473, D:P.473, D:I.475, D:I.477, F:L.20, F:I.27

9 x LHG: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE(Covalent)(Non-covalent)

LHG.2: 18 residues within 4Å: Chain A: L.27, P.31, M.34 Chain C: F.14, Y.19, E.20, F.22, L.23, L.26, I.28 Chain G: A.4, T.7, Q.8, L.44, G.48, I.51, L.52 Ligands: AJP.63 14 PLIP interactions: 5 interactions with chain C, 6 interactions with chain G, 3 interactions with chain A Hydrophobic interactions: C:F.14, C:F.22, C:L.23, C:L.26, C:I.28, G:T.7, G:L.44, G:I.51, G:L.52, A:L.27, A:P.31, A:P.31 Hydrogen bonds: G:T.7, G:Q.8 LHG.11: 8 residues within 4Å: Chain B: R.41, W.42, Y.45, V.49, G.52, T.57 Ligands: PQN.10, AJP.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.49, B:T.57 Hydrogen bonds: B:R.41 LHG.12: 15 residues within 4Å: Chain B: D.2, A.7, A.12, G.13, I.15, L.16, T.19, I.22, L.26, F.125 Chain C: E.108, I.111 Chain G: L.144, L.145, E.148 11 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C, 3 interactions with chain G Hydrophobic interactions: B:I.15, B:I.15, B:T.19, B:I.22, B:L.26, B:F.125, C:E.108, C:I.111, G:L.144, G:L.145, G:E.148 LHG.13: 4 residues within 4Å: Chain B: R.458, Q.461, V.462 Ligands: PQN.10 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.458, B:R.458, B:R.458 LHG.29: 14 residues within 4Å: Chain B: Y.366, Q.367, P.370, L.374, P.388, S.472, I.476 Chain D: P.22, K.112, R.114, L.115, F.118, L.119, A.122 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain D Hydrophobic interactions: B:P.388, B:I.476, D:R.114, D:L.115, D:F.118, D:F.118, D:F.118, D:L.119, D:A.122 LHG.30: 18 residues within 4Å: Chain D: F.46, P.461, V.464, F.465, A.468, C.469, V.472 Chain F: F.24, A.28, F.29 Chain P: L.11, M.14, V.17, F.18, L.21, F.25 Ligands: LHG.46, BCR.74 9 PLIP interactions: 4 interactions with chain D, 1 interactions with chain F, 4 interactions with chain P Hydrophobic interactions: D:F.46, D:F.465, D:A.468, D:V.472, F:F.24, P:L.11, P:V.17, P:F.18, P:L.21 LHG.45: 13 residues within 4Å: Chain F: F.303, T.307, I.310, T.311, F.444, R.448, Y.555, P.562, Q.563, I.565, A.566, L.572, Y.573 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.303, F:T.307, F:I.310, F:F.444, F:F.444, F:L.572 Hydrogen bonds: F:T.311, F:Y.555, F:P.562, F:Q.563 Salt bridges: F:R.448 LHG.46: 8 residues within 4Å: Chain F: W.9, F.24 Chain P: P.9, I.10 Ligands: LHG.30, AJP.40, AJP.54, BCR.74 4 PLIP interactions: 1 interactions with chain P, 3 interactions with chain F Hydrophobic interactions: P:I.10, F:W.9, F:F.24, F:F.24 LHG.69: 12 residues within 4Å: Chain A: F.216, L.217, W.220, L.328, V.332, Q.339, D.342, L.343 Chain H: I.199, R.202 Chain I: Y.10, S.17 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.216, A:L.217, A:L.217, A:L.328, A:V.332 Hydrogen bonds: A:D.342

2 x DGD: DIGALACTOSYL DIACYL GLYCEROL (DGDG)(Non-covalent)(Covalent)

DGD.3: 18 residues within 4Å: Chain A: D.6, L.7, Q.8, W.29, P.33, M.36, G.44, F.119, N.122, L.123, L.124, I.125, L.315 Chain C: Y.21 Chain L: E.6, T.52, F.53 Ligands: DGD.4 9 PLIP interactions: 1 interactions with chain C, 6 interactions with chain A, 2 interactions with chain L Hydrogen bonds: C:Y.21, A:L.7, A:Q.8, A:I.125 Hydrophobic interactions: A:W.29, A:F.119, A:L.315, L:E.6, L:T.52 DGD.4: 17 residues within 4Å: Chain A: I.5, L.7, G.120, Q.121, N.122, L.123, W.280, E.297, Q.303, I.304, A.307, V.308 Chain L: Y.13, A.17, Y.20 Ligands: BCR.1, DGD.3 9 PLIP interactions: 3 interactions with chain L, 6 interactions with chain A Hydrophobic interactions: L:Y.13, L:A.17, L:Y.20, A:L.123, A:V.308 Hydrogen bonds: A:Q.121, A:W.280, A:E.297, A:E.297

60 x AJP: Digitonin(Non-covalent)(Covalent)(Non-functional Binders)

AJP.5: 6 residues within 4Å: Chain A: L.362, F.366, V.368, A.369, F.370 Ligands: AJP.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.362, A:F.366, A:F.366, A:A.369, A:F.370 AJP.6: 7 residues within 4Å: Chain A: Q.201, Y.202, L.205, S.206, R.211, A.369 Ligands: AJP.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.202 Hydrogen bonds: A:L.205, A:R.211 AJP.7: 5 residues within 4Å: Chain A: Y.202, L.205, P.283, I.284, P.285 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.202, A:P.285 AJP.8: 5 residues within 4Å: Chain A: L.357, G.361, A.365 Ligands: AJP.9, AJP.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.357, A:A.365 AJP.9: 3 residues within 4Å: Chain A: A.365, F.366 Ligands: AJP.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.365, A:F.366, A:F.366 AJP.15: 6 residues within 4Å: Chain B: I.59, W.62, F.82, L.334, L.484 Ligands: AJP.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.59, B:I.59, B:W.62, B:W.62, B:F.82, B:L.334, B:L.484 AJP.16: 7 residues within 4Å: Chain B: L.89, F.338, P.480, L.481, L.484 Ligands: AJP.15, AJP.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.89, B:P.480, B:L.484 AJP.17: 8 residues within 4Å: Chain B: A.470, L.473, A.474, L.477, P.480, L.481 Ligands: AJP.16, AJP.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.470 AJP.18: 6 residues within 4Å: Chain B: L.477, N.479, P.480 Ligands: AJP.17, AJP.31, AJP.32 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.477, B:N.479 AJP.19: 4 residues within 4Å: Chain B: P.370, L.374 Chain D: P.22, F.23 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:P.22, D:P.22, D:F.23, B:P.370 AJP.20: 7 residues within 4Å: Chain B: L.30, I.34 Chain C: V.117, V.118, V.121, R.125 Ligands: AJP.28 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.117, C:V.118, B:L.30, B:I.34 AJP.21: 5 residues within 4Å: Chain B: V.27, L.30, A.31, Q.35 Ligands: AJP.22 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.27, B:L.30, B:L.30 Hydrogen bonds: B:Q.35, B:Q.35 AJP.22: 2 residues within 4Å: Ligands: LHG.11, AJP.21 No protein-ligand interaction detected (PLIP) AJP.23: 6 residues within 4Å: Chain B: G.409, L.413, L.416 Ligands: AJP.25, AJP.38, AJP.42 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.413, B:L.416 AJP.24: 7 residues within 4Å: Chain B: L.276, T.279, V.280, I.283, L.284 Chain F: F.652 Ligands: AJP.25 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.276, B:V.280, B:V.280, B:I.283, B:L.284 AJP.25: 7 residues within 4Å: Chain B: I.283, I.287, L.410, L.413, L.416 Ligands: AJP.23, AJP.24 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.283, B:I.283, B:I.287, B:I.287, B:L.413, B:L.413 Hydrogen bonds: B:L.410 AJP.26: 3 residues within 4Å: Chain B: D.2 Chain C: L.110 Ligands: AJP.8 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.110 AJP.27: 8 residues within 4Å: Chain A: K.346, P.350, V.351, V.354 Chain C: W.124 Chain I: I.7, Y.10 Ligands: AJP.28 6 PLIP interactions: 3 interactions with chain A, 2 interactions with chain I, 1 interactions with chain C Hydrophobic interactions: A:P.350, A:V.351, A:V.354, I:I.7, I:Y.10, C:W.124 AJP.28: 7 residues within 4Å: Chain A: V.354 Chain C: V.117, V.121, W.124, R.125 Ligands: AJP.20, AJP.27 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:V.354, C:V.117, C:V.121, C:W.124, C:W.124 Hydrogen bonds: C:R.125 AJP.31: 9 residues within 4Å: Chain B: I.476, L.477 Chain D: L.12, Y.70, D.71, W.72, W.80 Ligands: AJP.18, AJP.32 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.12, D:L.12, D:Y.70, D:Y.70, D:W.80 Hydrogen bonds: B:I.476 AJP.32: 6 residues within 4Å: Chain B: I.476 Chain D: L.12, Y.70 Ligands: AJP.18, AJP.31, AJP.33 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:Y.70, B:I.476 AJP.33: 5 residues within 4Å: Chain D: F.4, T.9, F.13, V.16 Ligands: AJP.32 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.4, D:V.16, D:V.16 AJP.34: 5 residues within 4Å: Chain D: A.47, L.48, Y.51 Ligands: AJP.35, AJP.39 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.51 AJP.35: 6 residues within 4Å: Chain D: A.47, Y.51 Chain P: L.12, T.15, I.19 Ligands: AJP.34 4 PLIP interactions: 1 interactions with chain P, 3 interactions with chain D Hydrophobic interactions: P:I.19, D:A.47, D:Y.51 Hydrogen bonds: D:Y.51 AJP.36: 2 residues within 4Å: Chain D: L.413 Ligands: AJP.51 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.413, D:L.413, D:L.413 AJP.37: 6 residues within 4Å: Chain D: L.219, L.231, F.277, V.280 Chain Q: L.40 Ligands: AJP.41 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain Q Hydrophobic interactions: D:L.219, D:L.231, D:F.277, D:F.277, D:F.277, Q:L.40 AJP.38: 13 residues within 4Å: Chain B: W.403, Y.408 Chain D: F.179, V.182, A.186, Y.190, F.210, L.213, G.217, V.220 Ligands: AJP.23, AJP.41, AJP.42 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.179, D:F.179, D:A.186, D:F.210, D:V.220, B:Y.408 AJP.39: 5 residues within 4Å: Chain D: S.2, W.6, F.13, F.56 Ligands: AJP.34 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.6, D:W.6, D:F.13 Hydrogen bonds: D:S.2 AJP.40: 6 residues within 4Å: Chain D: L.479, Y.480 Chain F: W.75, I.149 Ligands: LHG.46, AJP.54 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:I.149, F:I.149, D:L.479, D:L.479, D:Y.480 AJP.41: 9 residues within 4Å: Chain D: L.208, G.209, L.212, L.213, A.216, F.277 Ligands: AJP.37, AJP.38, AJP.42 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.212, D:L.212, D:A.216, D:F.277 Hydrogen bonds: D:G.209 AJP.42: 4 residues within 4Å: Chain D: L.213 Ligands: AJP.23, AJP.38, AJP.41 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.213, D:L.213 AJP.43: 5 residues within 4Å: Chain E: Y.5, I.8 Chain G: F.108, T.112 Ligands: AJP.66 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:F.108, G:F.108, G:T.112, E:Y.5 AJP.49: 5 residues within 4Å: Chain F: L.4, A.49, G.53, T.57 Ligands: AJP.58 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.4, F:T.57 AJP.50: 7 residues within 4Å: Chain F: F.29, T.32, T.33, L.36, S.40 Ligands: AJP.56, AJP.57 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.29, F:F.29, F:L.36 AJP.51: 9 residues within 4Å: Chain D: V.417 Chain F: G.195, W.198, A.199, L.221, L.225, I.228, L.229 Ligands: AJP.36 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:W.198, F:W.198, F:W.198, F:A.199, F:L.221, F:L.225, F:L.225, F:I.228, F:L.229 Hydrogen bonds: F:G.195 AJP.52: 4 residues within 4Å: Chain F: F.244, T.293, W.296, F.300 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.244, F:F.244, F:F.300 AJP.53: 6 residues within 4Å: Chain F: G.611, N.614, L.615, F.618 Ligands: SQD.14, AJP.76 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:N.614, F:F.618 AJP.54: 8 residues within 4Å: Chain F: W.9, Q.71, G.86, Y.87, G.137, F.150 Ligands: AJP.40, LHG.46 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:W.9, F:Y.87, F:F.150 Hydrogen bonds: F:Q.71 AJP.55: 5 residues within 4Å: Chain F: G.626, L.627, Y.629, L.630 Ligands: AJP.61 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:Y.629, F:Y.629, F:Y.629 AJP.56: 2 residues within 4Å: Ligands: AJP.50, AJP.57 No protein-ligand interaction detected (PLIP) AJP.57: 5 residues within 4Å: Chain F: L.36, P.39, F.43 Ligands: AJP.50, AJP.56 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.36, F:P.39, F:F.43 AJP.58: 4 residues within 4Å: Chain F: L.4, L.10 Ligands: AJP.49, AJP.59 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.4, F:L.10 AJP.59: 3 residues within 4Å: Chain F: Y.7, L.10 Ligands: AJP.58 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.7 AJP.60: 3 residues within 4Å: Chain F: Y.581, L.585, V.589 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.581, F:L.585 AJP.61: 6 residues within 4Å: Chain F: V.622, T.623, E.625, G.626, L.627 Ligands: AJP.55 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.627 Hydrogen bonds: F:E.625 AJP.62: 9 residues within 4Å: Chain A: L.101, V.105, M.148 Chain G: L.29, Y.34, F.37, L.38, G.41, L.44 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:Y.34, G:F.37, G:L.38 AJP.63: 9 residues within 4Å: Chain A: L.27 Chain C: L.23 Chain G: L.3, L.6, T.7, I.10, T.11 Ligands: LHG.2, AJP.64 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:L.6, G:T.7, G:T.11, C:L.23 AJP.64: 4 residues within 4Å: Chain G: L.6, I.10 Ligands: AJP.63, AJP.65 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.6 AJP.65: 4 residues within 4Å: Chain G: I.10, F.13 Ligands: AJP.64, AJP.68 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:I.10, G:I.10, G:F.13, G:F.13 AJP.66: 4 residues within 4Å: Chain G: F.108, T.112, L.116 Ligands: AJP.43 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.116 AJP.67: 6 residues within 4Å: Chain E: L.12, C.15, Y.19 Chain G: L.24, W.94, A.101 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:A.101 AJP.68: 3 residues within 4Å: Chain E: Y.5 Chain G: F.13 Ligands: AJP.65 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.13 AJP.75: 4 residues within 4Å: Chain D: L.413 Chain Q: F.31, W.38 Ligands: AJP.81 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:F.31 AJP.76: 8 residues within 4Å: Chain F: V.608 Chain Q: D.16, P.18, I.21, A.22, L.29 Ligands: AJP.53, AJP.78 6 PLIP interactions: 5 interactions with chain Q, 1 interactions with chain F Hydrophobic interactions: Q:P.18, Q:I.21, Q:A.22, Q:L.29, F:V.608 Hydrogen bonds: Q:P.18 AJP.77: 5 residues within 4Å: Chain D: P.230 Chain Q: I.32, I.36, W.37, H.41 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain D Hydrophobic interactions: Q:I.32, Q:I.36, D:P.230 AJP.78: 3 residues within 4Å: Chain Q: P.18, A.22 Ligands: AJP.76 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:P.18 AJP.79: 4 residues within 4Å: Chain Q: A.19, M.20, I.23 Ligands: AJP.80 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:A.19 AJP.80: 7 residues within 4Å: Chain F: R.596, L.597, Q.600 Chain Q: M.20, L.27, I.28 Ligands: AJP.79 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain Q Hydrophobic interactions: F:L.597, Q:L.27, Q:I.28 AJP.81: 4 residues within 4Å: Chain Q: G.34, W.37, W.38 Ligands: AJP.75 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:W.37 AJP.82: 3 residues within 4Å: Chain Q: G.30, A.33, W.37 3 PLIP interactions: 3 interactions with chain Q Hydrophobic interactions: Q:A.33, Q:W.37, Q:W.37

1 x PQN: PHYLLOQUINONE(Covalent)

PQN.10: 14 residues within 4Å: Chain B: Y.45, L.89, L.92, L.341, S.453, F.455, G.456, R.458, P.459, V.462, M.466, T.467 Ligands: LHG.11, LHG.13 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.92, B:L.341, B:P.459, B:P.459, B:V.462 Hydrogen bonds: B:G.456

4 x SQD: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL(Non-covalent)(Covalent)

SQD.14: 17 residues within 4Å: Chain B: V.419, I.420, Y.423, K.430 Chain D: Q.163, Y.164, T.167, K.168, L.171, G.175, V.224, P.230, L.231 Chain F: V.613, T.616, T.620 Ligands: AJP.53 12 PLIP interactions: 3 interactions with chain B, 6 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: B:V.419, B:I.420, D:K.168, D:L.171, D:V.224, D:L.231, F:V.613, F:V.613, F:T.620 Salt bridges: B:K.430 Hydrogen bonds: D:Q.163, D:T.167 SQD.47: 20 residues within 4Å: Chain D: K.373, F.376, A.377, T.380, L.384 Chain F: L.20, G.23, L.26, S.30, E.31, S.34, G.120, R.123, A.126, Y.127, L.130, M.156, L.160, Y.166 Ligands: BCR.74 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:L.20, F:L.26, F:A.126, F:Y.127, F:L.130, F:L.160, F:L.160, D:F.376, D:A.377, D:L.384 Hydrogen bonds: F:S.30, F:E.31, F:S.34 Salt bridges: F:R.123, F:R.123 SQD.48: 13 residues within 4Å: Chain D: Y.297, I.432, S.436, R.439 Chain F: Q.176, K.177, Y.586, E.587, F.590, I.591, R.595 Chain Q: I.9 Ligands: BCR.44 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:Y.297, D:S.436, D:R.439, D:R.439 Hydrophobic interactions: F:Y.586, F:F.590 Salt bridges: F:R.595 SQD.73: 15 residues within 4Å: Chain A: I.68, L.74, L.77, L.81, I.84 Chain K: V.34, W.37 Chain L: P.63, I.65, N.66, R.68 Chain N: L.4, F.29, R.32, V.138 13 PLIP interactions: 3 interactions with chain L, 4 interactions with chain A, 4 interactions with chain N, 2 interactions with chain K Hydrophobic interactions: L:P.63, A:L.74, A:L.77, A:L.81, A:I.84, N:L.4, N:L.4, K:W.37, K:W.37 Salt bridges: L:R.68, L:R.68, N:R.32, N:R.32

3 x SF4: IRON/SULFUR CLUSTER(Non-covalent)(Covalent)

SF4.70: 7 residues within 4Å: Chain I: C.73, I.98, C.103, I.104, C.106, A.107, C.109 3 PLIP interactions: 3 interactions with chain I, Metal complexes: I:C.73, I:C.103, I:C.109 SF4.71: 11 residues within 4Å: Chain I: F.58, C.63, I.64, A.65, C.66, E.67, V.68, C.69, C.113, T.115, C.117 2 PLIP interactions: 2 interactions with chain I, Metal complexes: I:C.63, I:C.66 SF4.72: 10 residues within 4Å: Chain H: R.69 Chain K: A.51, C.52, C.53, G.88, T.89, A.116, C.117, C.148, P.149 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.52, K:C.53, K:C.117, K:C.148

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.83: 9 residues within 4Å: Chain R: F.39, S.40, C.41, R.42, A.43, C.46, T.48, C.49, C.79 2 PLIP interactions: 2 interactions with chain R, Metal complexes: R:T.48, R:C.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, C. et al., Structural insights into NDH-1 mediated cyclic electron transfer. Nat Commun (2020)

Release Date

2020-02-19

Peptides

NAD(P)H-quinone oxidoreductase subunit 1: A
NAD(P)H-quinone oxidoreductase subunit 2: B
NAD(P)H-quinone oxidoreductase subunit 3: C
NAD(P)H-quinone oxidoreductase chain 4 1: D
NAD(P)H-quinone oxidoreductase subunit 4L: E
NADH dehydrogenase subunit 5: F
NADH-quinone oxidoreductase subunit J: G
NAD(P)H-quinone oxidoreductase subunit H: H
NAD(P)H-quinone oxidoreductase subunit I: I
NAD(P)H-quinone oxidoreductase subunit J: J
NAD(P)H-quinone oxidoreductase subunit K: K
NAD(P)H-quinone oxidoreductase subunit L: L
NAD(P)H-quinone oxidoreductase subunit M: M
NAD(P)H-quinone oxidoreductase subunit N: N
NAD(P)H-quinone oxidoreductase subunit O: O
NAD(P)H-quinone oxidoreductase subunit P: P
NAD(P)H-quinone oxidoreductase subunit Q: Q
Ferredoxin-1: R
Tlr0636 protein: S
Tlr0472 protein: T

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
V

Membrane

We predict this structure to be a membrane protein.
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NAD(P)H-quinone oxidoreductase subunit 1

NAD(P)H-quinone oxidoreductase subunit 2

NAD(P)H-quinone oxidoreductase subunit 3

NAD(P)H-quinone oxidoreductase chain 4 1

NAD(P)H-quinone oxidoreductase subunit 4L

NADH dehydrogenase subunit 5

NADH-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit H

NAD(P)H-quinone oxidoreductase subunit I

NAD(P)H-quinone oxidoreductase subunit J

NAD(P)H-quinone oxidoreductase subunit K

NAD(P)H-quinone oxidoreductase subunit L

NAD(P)H-quinone oxidoreductase subunit M

NAD(P)H-quinone oxidoreductase subunit N

NAD(P)H-quinone oxidoreductase subunit O

NAD(P)H-quinone oxidoreductase subunit P

NAD(P)H-quinone oxidoreductase subunit Q

Ferredoxin-1

Tlr0636 protein

Tlr0472 protein

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