- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)
- 1 x OAA: OXALOACETATE ION(Non-covalent)
OAA.2: 12 residues within 4Å:- Chain A: G.62, F.130, H.253, L.263, T.265, E.266, R.297, H.364, R.408, G.410, A.411
- Ligands: FAD.1
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:F.130
- Hydrogen bonds: A:G.62, A:E.266, A:R.297, A:A.411
- Salt bridges: A:H.253, A:R.297, A:R.297, A:H.364, A:R.408
- 1 x K: POTASSIUM ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 63 x UNL: UNKNOWN LIGAND(Non-functional Binders)
UNL.7: 10 residues within 4Å:- Chain A: K.49, L.50, I.196, T.228, W.515, T.517, V.520, E.521, E.524
- Chain B: R.63
Ligand excluded by PLIPUNL.8: 5 residues within 4Å:- Chain A: R.557, D.559, F.561, D.562, Y.563
Ligand excluded by PLIPUNL.9: 1 residues within 4Å:- Chain A: F.137
Ligand excluded by PLIPUNL.10: 5 residues within 4Å:- Chain A: R.152, A.334, P.338
- Chain B: D.153, E.157
Ligand excluded by PLIPUNL.11: 5 residues within 4Å:- Chain A: E.560, K.572, R.580, P.600, V.601
Ligand excluded by PLIPUNL.12: 8 residues within 4Å:- Chain A: M.367, A.399, S.400, A.401, S.402, V.403, H.404, G.405
Ligand excluded by PLIPUNL.13: 3 residues within 4Å:- Chain A: E.494, S.497, R.501
Ligand excluded by PLIPUNL.14: 7 residues within 4Å:- Chain A: R.218, F.221, C.223, H.227, G.259, A.260
- Chain B: R.66
Ligand excluded by PLIPUNL.15: 8 residues within 4Å:- Chain A: C.244, Q.245, D.246, L.247, E.248, Q.534, T.583, S.585
Ligand excluded by PLIPUNL.16: 3 residues within 4Å:- Chain A: S.118, R.119
- Chain B: R.149
Ligand excluded by PLIPUNL.17: 3 residues within 4Å:- Chain A: R.32, G.36, E.39
Ligand excluded by PLIPUNL.18: 5 residues within 4Å:- Chain A: R.152, G.339, E.342, T.343
- Chain B: K.227
Ligand excluded by PLIPUNL.19: 8 residues within 4Å:- Chain A: D.92, D.94, A.95, T.372, N.373, Y.374, A.401, I.602
Ligand excluded by PLIPUNL.20: 4 residues within 4Å:- Chain A: D.94, Y.374, R.604, T.605
Ligand excluded by PLIPUNL.21: 7 residues within 4Å:- Chain A: Q.377, V.388, V.389, P.390, G.391, L.392, Y.393
Ligand excluded by PLIPUNL.22: 8 residues within 4Å:- Chain A: R.464, T.465, S.466, K.507, T.508, F.509, D.518
- Chain B: S.57
Ligand excluded by PLIPUNL.23: 3 residues within 4Å:- Chain A: E.608, E.609, S.612
Ligand excluded by PLIPUNL.24: 3 residues within 4Å:- Chain A: Y.98, Q.102, R.422
Ligand excluded by PLIPUNL.25: 5 residues within 4Å:- Chain A: E.18, F.19, D.20, N.43, V.438
Ligand excluded by PLIPUNL.26: 2 residues within 4Å:- Chain A: K.85, G.138
Ligand excluded by PLIPUNL.27: 5 residues within 4Å:- Chain A: Y.176, C.195, E.197
- Ligands: UNL.28, UNL.29
Ligand excluded by PLIPUNL.28: 4 residues within 4Å:- Chain A: Y.176, E.197
- Ligands: UNL.27, UNL.29
Ligand excluded by PLIPUNL.29: 4 residues within 4Å:- Chain A: V.174, Y.176
- Ligands: UNL.27, UNL.28
Ligand excluded by PLIPUNL.30: 2 residues within 4Å:- Chain A: I.618, R.619
Ligand excluded by PLIPUNL.31: 1 residues within 4Å:- Ligands: UNL.32
Ligand excluded by PLIPUNL.32: 3 residues within 4Å:- Chain A: F.575, E.576
- Ligands: UNL.31
Ligand excluded by PLIPUNL.36: 6 residues within 4Å:- Chain B: H.104, M.105, Y.106, Y.171
- Chain C: F.12, W.13
Ligand excluded by PLIPUNL.37: 4 residues within 4Å:- Chain A: R.54, E.175
- Chain B: R.62, Y.119
Ligand excluded by PLIPUNL.38: 2 residues within 4Å:- Ligands: UNL.40, UNL.68
Ligand excluded by PLIPUNL.39: 3 residues within 4Å:- Chain B: K.151, I.192, S.194
Ligand excluded by PLIPUNL.40: 4 residues within 4Å:- Chain B: H.104, W.173
- Ligands: UNL.38, UNL.68
Ligand excluded by PLIPUNL.41: 5 residues within 4Å:- Chain B: R.62, S.72, A.74, P.113, L.115
Ligand excluded by PLIPUNL.42: 4 residues within 4Å:- Chain B: Y.188, I.192, E.237, M.241
Ligand excluded by PLIPUNL.43: 3 residues within 4Å:- Chain B: D.176, K.177
- Chain C: M.9
Ligand excluded by PLIPUNL.44: 6 residues within 4Å:- Chain B: I.125, E.126, K.130, E.201, R.202, Q.205
Ligand excluded by PLIPUNL.45: 3 residues within 4Å:- Chain B: T.82, T.86, K.87
Ligand excluded by PLIPUNL.46: 4 residues within 4Å:- Chain B: E.140, Q.141, Y.142
- Ligands: UNL.47
Ligand excluded by PLIPUNL.47: 4 residues within 4Å:- Chain B: K.131, Y.142, L.143
- Ligands: UNL.46
Ligand excluded by PLIPUNL.48: 4 residues within 4Å:- Chain B: T.32, Y.33, E.34, L.55
Ligand excluded by PLIPUNL.49: 3 residues within 4Å:- Chain B: G.68, P.226, K.227
Ligand excluded by PLIPUNL.50: 3 residues within 4Å:- Chain B: N.220, R.223
- Chain C: S.33
Ligand excluded by PLIPUNL.54: 5 residues within 4Å:- Chain A: Y.162, Y.172
- Chain B: Y.119, K.123
- Chain C: E.8
Ligand excluded by PLIPUNL.55: 3 residues within 4Å:- Chain B: D.176
- Chain C: W.13
- Ligands: UNL.75
Ligand excluded by PLIPUNL.56: 10 residues within 4Å:- Chain C: V.53, F.56, L.83, S.86, A.87, A.90, L.91
- Chain D: L.43, L.100
- Ligands: 3PE.62
Ligand excluded by PLIPUNL.57: 6 residues within 4Å:- Chain C: V.92, S.96, T.99, W.100, I.137
- Chain D: L.21
Ligand excluded by PLIPUNL.58: 1 residues within 4Å:- Chain C: F.93
Ligand excluded by PLIPUNL.59: 5 residues within 4Å:- Chain B: Y.100, P.101, P.103
- Chain C: S.24, P.25
Ligand excluded by PLIPUNL.60: 7 residues within 4Å:- Chain C: L.34, P.35, M.38, R.104, V.119, E.120, G.123
Ligand excluded by PLIPUNL.61: 2 residues within 4Å:- Chain C: I.84, K.88
Ligand excluded by PLIPUNL.63: 4 residues within 4Å:- Chain D: H.9, H.48, W.49, Y.73
Ligand excluded by PLIPUNL.64: 7 residues within 4Å:- Chain C: S.50, S.54
- Chain D: T.44, G.47, H.48, S.76, T.79
Ligand excluded by PLIPUNL.65: 2 residues within 4Å:- Chain C: I.40
- Chain D: Y.58
Ligand excluded by PLIPUNL.66: 6 residues within 4Å:- Chain B: Y.213
- Chain D: A.6, H.9, W.10, E.13, Q.53
Ligand excluded by PLIPUNL.67: 1 residues within 4Å:- Chain D: Y.88
Ligand excluded by PLIPUNL.68: 3 residues within 4Å:- Chain D: Y.58
- Ligands: UNL.38, UNL.40
Ligand excluded by PLIPUNL.69: 3 residues within 4Å:- Chain D: L.19, S.38
- Ligands: UNL.70
Ligand excluded by PLIPUNL.70: 3 residues within 4Å:- Chain D: A.34, S.38
- Ligands: UNL.69
Ligand excluded by PLIPUNL.71: 7 residues within 4Å:- Chain D: Y.30, G.32, P.33, A.34, V.35, Y.37
- Ligands: UNL.72
Ligand excluded by PLIPUNL.72: 5 residues within 4Å:- Chain D: P.33, Y.37, Y.88
- Ligands: UNL.71, UNL.73
Ligand excluded by PLIPUNL.73: 4 residues within 4Å:- Chain D: C.84, Y.88, Y.89
- Ligands: UNL.72
Ligand excluded by PLIPUNL.74: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.75: 2 residues within 4Å:- Chain D: H.60
- Ligands: UNL.55
Ligand excluded by PLIPUNL.76: 1 residues within 4Å:- Chain D: H.60
Ligand excluded by PLIP- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x F3S: FE3-S4 CLUSTER(Non-covalent)
- 1 x TTF: 4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE(Non-covalent)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.52: 19 residues within 4Å:- Chain B: H.216
- Chain C: H.42, R.43, G.46, V.47, L.49, S.50, H.98, T.99, G.102, H.105
- Chain D: R.14, S.17, L.20, L.24, L.43, H.46, G.50, L.51
20 PLIP interactions:10 interactions with chain D, 1 interactions with chain B, 9 interactions with chain C,- Hydrophobic interactions: D:L.20, D:L.24, D:L.43, D:L.51, C:L.49, C:T.99, C:H.105
- Hydrogen bonds: D:G.50
- Water bridges: D:R.14, D:R.14, D:R.14, C:H.105, C:H.105
- Salt bridges: D:R.14, B:H.216, C:R.43, C:H.105
- Metal complexes: D:H.46, C:H.98
- pi-Stacking: C:H.42
- 1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
UMQ.53: 10 residues within 4Å:- Chain B: R.223
- Chain C: K.31, W.32, S.33, L.34, P.35, A.37, T.41, F.93, E.120
12 PLIP interactions:9 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:L.34, C:A.37, C:T.41, C:F.93
- Hydrogen bonds: C:K.31, C:K.31, C:L.34, C:E.120, B:R.223
- Water bridges: C:W.32, B:R.223
- Salt bridges: B:R.223
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.62: 16 residues within 4Å:- Chain C: L.49, G.52, V.53, L.91, L.95, I.137, M.140
- Chain D: A.27, Y.28, L.39, I.93, C.94, V.97, A.98, W.101
- Ligands: UNL.56
9 PLIP interactions:5 interactions with chain C, 4 interactions with chain D- Hydrophobic interactions: C:L.49, C:V.53, C:L.91, C:L.95, C:I.137, D:A.27, D:L.39, D:I.93, D:W.101
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, L.S. et al., Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors. Biochim Biophys Acta Proteins Proteom (2021)
- Release Date
- 2019-11-06
- Peptides
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Succinate dehydrogenase cytochrome b, large subunit: C
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)
- 1 x OAA: OXALOACETATE ION(Non-covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- 1 x MG: MAGNESIUM ION(Non-covalent)
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 63 x UNL: UNKNOWN LIGAND(Non-functional Binders)
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x F3S: FE3-S4 CLUSTER(Non-covalent)
- 1 x TTF: 4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE(Non-covalent)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, L.S. et al., Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors. Biochim Biophys Acta Proteins Proteom (2021)
- Release Date
- 2019-11-06
- Peptides
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Succinate dehydrogenase cytochrome b, large subunit: C
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.