- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.97 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: 13 residues within 4Å:- Chain A: Q.61, 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
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:F.130
- Hydrogen bonds: A:G.62, A:E.266, A:R.297, A:R.297, A:A.411
- Salt bridges: A:H.253, A:R.297, A:R.297, A:H.364, A:R.408
- 2 x K: POTASSIUM ION(Non-covalent)
K.3: 6 residues within 4Å:- Chain A: Y.365, N.366, M.367, G.368, E.397, A.399
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:N.366, A:M.367, A:G.368, A:E.397, A:A.399
K.37: 5 residues within 4Å:- Chain B: M.191, D.193, D.196, T.199
- Ligands: UNL.39
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.193, B:D.196, B:T.199, H2O.12
- 80 x UNL: UNKNOWN LIGAND(Non-functional Binders)
UNL.4: 4 residues within 4Å:- Chain A: Q.498, D.502, A.504, H.505
Ligand excluded by PLIPUNL.6: 7 residues within 4Å:- Chain A: K.49, T.228, W.515, T.517, E.521, E.524
- Chain B: R.63
Ligand excluded by PLIPUNL.7: 4 residues within 4Å:- Chain A: Y.81, F.137, S.612, V.614
Ligand excluded by PLIPUNL.8: 6 residues within 4Å:- Chain A: R.218, H.227, A.260
- Chain B: R.66
- Ligands: UNL.12, UNL.48
Ligand excluded by PLIPUNL.9: 3 residues within 4Å:- Chain A: R.152, A.334
- Chain B: E.157
Ligand excluded by PLIPUNL.10: 6 residues within 4Å:- Chain A: E.560, K.572, R.580, P.600, V.601
- Ligands: UNL.29
Ligand excluded by PLIPUNL.11: 5 residues within 4Å:- Chain A: S.497, R.501, S.591, G.592, K.593
Ligand excluded by PLIPUNL.12: 3 residues within 4Å:- Chain A: F.221, G.259
- Ligands: UNL.8
Ligand excluded by PLIPUNL.13: 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.14: 5 residues within 4Å:- Chain A: K.543, E.576, E.577, H.578, W.579
Ligand excluded by PLIPUNL.15: 5 residues within 4Å:- Chain A: E.197
- Chain B: V.108, D.114, S.116
- Chain C: K.15
Ligand excluded by PLIPUNL.16: 1 residues within 4Å:- Chain A: Y.586
Ligand excluded by PLIPUNL.17: 4 residues within 4Å:- Chain A: E.72, D.73, W.78, L.135
Ligand excluded by PLIPUNL.18: 3 residues within 4Å:- Chain A: W.78, Q.136, F.137
Ligand excluded by PLIPUNL.19: 5 residues within 4Å:- Chain A: R.557, D.559, F.561, D.562, Y.563
Ligand excluded by PLIPUNL.20: 8 residues within 4Å:- Chain A: R.54, S.55, H.56, A.59, A.226
- Chain B: S.64, C.65, C.70
Ligand excluded by PLIPUNL.21: 7 residues within 4Å:- Chain A: L.50, F.51, R.54, E.175
- Chain B: R.62, S.72
- Ligands: UNL.41
Ligand excluded by PLIPUNL.22: 5 residues within 4Å:- Chain A: E.121, E.122, G.123
- Chain B: L.143, S.145
Ligand excluded by PLIPUNL.23: 4 residues within 4Å:- Chain A: G.69, N.70, M.71, E.72
Ligand excluded by PLIPUNL.24: 3 residues within 4Å:- Chain A: K.375, T.427, E.430
Ligand excluded by PLIPUNL.25: 1 residues within 4Å:- Chain A: Q.11
Ligand excluded by PLIPUNL.26: 2 residues within 4Å:- Chain A: T.462, H.505
Ligand excluded by PLIPUNL.27: 2 residues within 4Å:- Chain A: R.32, R.422
Ligand excluded by PLIPUNL.28: 1 residues within 4Å:- Chain A: N.383
Ligand excluded by PLIPUNL.29: 3 residues within 4Å:- Chain A: F.575, H.578
- Ligands: UNL.10
Ligand excluded by PLIPUNL.30: 2 residues within 4Å:- Chain A: E.608, S.613
Ligand excluded by PLIPUNL.31: 3 residues within 4Å:- Chain A: I.602, D.603, R.604
Ligand excluded by PLIPUNL.32: 4 residues within 4Å:- Chain A: F.575, E.576, K.581, Y.598
Ligand excluded by PLIPUNL.33: 5 residues within 4Å:- Chain A: R.282, A.291, K.292, D.293, L.294
Ligand excluded by PLIPUNL.38: 6 residues within 4Å:- Chain B: H.104, M.105, Y.106
- Chain C: F.12, W.13, L.23
Ligand excluded by PLIPUNL.39: 4 residues within 4Å:- Chain B: K.151, I.192, S.194
- Ligands: K.37
Ligand excluded by PLIPUNL.40: 6 residues within 4Å:- Chain B: I.125, E.126, K.130, E.201, R.202, Q.205
Ligand excluded by PLIPUNL.41: 7 residues within 4Å:- Chain A: F.51, R.54, E.175
- Chain B: R.62, L.115, Y.119
- Ligands: UNL.21
Ligand excluded by PLIPUNL.42: 2 residues within 4Å:- Chain B: Q.150, K.151
Ligand excluded by PLIPUNL.43: 7 residues within 4Å:- Chain B: D.153, G.154, L.155, Y.188, N.230, K.233, A.234
Ligand excluded by PLIPUNL.44: 2 residues within 4Å:- Chain B: M.30, Y.100
Ligand excluded by PLIPUNL.45: 1 residues within 4Å:- Ligands: UNL.60
Ligand excluded by PLIPUNL.46: 5 residues within 4Å:- Chain B: C.40, G.41, D.46, I.49, K.50
Ligand excluded by PLIPUNL.47: 4 residues within 4Å:- Chain B: H.104, W.173
- Chain C: H.26
- Chain D: Y.58
Ligand excluded by PLIPUNL.48: 3 residues within 4Å:- Chain A: A.260
- Chain B: R.66
- Ligands: UNL.8
Ligand excluded by PLIPUNL.49: 5 residues within 4Å:- Chain A: T.343
- Chain B: E.67, G.68, I.69, K.227
Ligand excluded by PLIPUNL.50: 3 residues within 4Å:- Chain A: N.112
- Chain B: Q.137, Y.142
Ligand excluded by PLIPUNL.51: 2 residues within 4Å:- Chain B: T.222
- Ligands: UNL.69
Ligand excluded by PLIPUNL.52: 2 residues within 4Å:- Chain B: K.177, F.210
Ligand excluded by PLIPUNL.53: 7 residues within 4Å:- Chain B: P.169, W.173, I.218
- Chain C: S.39, I.40, R.43
- Chain D: Y.58
Ligand excluded by PLIPUNL.56: 3 residues within 4Å:- Chain A: Y.162
- Chain B: K.123
- Chain C: E.8
Ligand excluded by PLIPUNL.57: 6 residues within 4Å:- Chain C: F.56, L.91
- Chain D: L.43, I.93, L.100
- Ligands: 3PE.76
Ligand excluded by PLIPUNL.58: 7 residues within 4Å:- Chain C: S.96, T.99, W.100, I.137
- Chain D: L.21, P.25
- Ligands: UNL.91
Ligand excluded by PLIPUNL.59: 2 residues within 4Å:- Chain C: T.41, G.44
Ligand excluded by PLIPUNL.60: 4 residues within 4Å:- Chain C: T.4, A.5, K.6
- Ligands: UNL.45
Ligand excluded by PLIPUNL.61: 2 residues within 4Å:- Chain B: D.176
- Chain C: W.13
Ligand excluded by PLIPUNL.62: 4 residues within 4Å:- Chain C: W.32, A.37, I.40
- Ligands: UMQ.55
Ligand excluded by PLIPUNL.63: 7 residues within 4Å:- Chain C: F.56, A.59, A.60, E.65, Q.66, F.67
- Chain D: D.90
Ligand excluded by PLIPUNL.64: 1 residues within 4Å:- Chain C: A.82
Ligand excluded by PLIPUNL.65: 3 residues within 4Å:- Chain C: R.104, S.122, V.126
Ligand excluded by PLIPUNL.66: 1 residues within 4Å:- Ligands: 3PE.76
Ligand excluded by PLIPUNL.67: 4 residues within 4Å:- Chain C: K.112, G.113, Q.118
- Ligands: UNL.73
Ligand excluded by PLIPUNL.68: 2 residues within 4Å:- Chain B: N.230
- Ligands: UNL.69
Ligand excluded by PLIPUNL.69: 4 residues within 4Å:- Chain C: K.115, L.116
- Ligands: UNL.51, UNL.68
Ligand excluded by PLIPUNL.70: 4 residues within 4Å:- Chain C: Q.66, P.68
- Chain D: D.90, V.91
Ligand excluded by PLIPUNL.71: 4 residues within 4Å:- Chain C: E.8, R.11, F.12, K.15
Ligand excluded by PLIPUNL.72: 1 residues within 4Å:- Chain C: G.44
Ligand excluded by PLIPUNL.73: 5 residues within 4Å:- Chain C: G.113, F.114, K.115, Q.118
- Ligands: UNL.67
Ligand excluded by PLIPUNL.74: 3 residues within 4Å:- Chain B: P.21
- Chain C: R.21
- Ligands: UNL.75
Ligand excluded by PLIPUNL.75: 3 residues within 4Å:- Chain C: S.19, S.20
- Ligands: UNL.74
Ligand excluded by PLIPUNL.77: 5 residues within 4Å:- Chain D: H.9, H.48, W.49, Y.73
- Ligands: UNL.90
Ligand excluded by PLIPUNL.78: 6 residues within 4Å:- Chain C: S.50, S.54
- Chain D: T.44, H.48, S.76, T.79
Ligand excluded by PLIPUNL.79: 4 residues within 4Å:- Chain D: A.41, T.44, L.45, F.80
Ligand excluded by PLIPUNL.80: 2 residues within 4Å:- Chain D: A.41, A.42
Ligand excluded by PLIPUNL.81: 3 residues within 4Å:- Chain D: A.34, S.38
- Ligands: UNL.82
Ligand excluded by PLIPUNL.82: 4 residues within 4Å:- Chain D: P.33, A.34
- Ligands: UNL.81, UNL.83
Ligand excluded by PLIPUNL.83: 4 residues within 4Å:- Chain D: Y.37, C.84, Y.88
- Ligands: UNL.82
Ligand excluded by PLIPUNL.84: 4 residues within 4Å:- Chain D: C.84, Y.85, Y.88, Y.89
Ligand excluded by PLIPUNL.85: 1 residues within 4Å:- Chain D: V.74
Ligand excluded by PLIPUNL.86: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.87: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.88: 4 residues within 4Å:- Chain D: A.6, H.9, W.10
- Ligands: UNL.89
Ligand excluded by PLIPUNL.89: 4 residues within 4Å:- Chain D: W.10, E.13, Q.53
- Ligands: UNL.88
Ligand excluded by PLIPUNL.90: 1 residues within 4Å:- Ligands: UNL.77
Ligand excluded by PLIPUNL.91: 4 residues within 4Å:- Chain D: A.18, L.21, G.22
- Ligands: UNL.58
Ligand excluded by PLIP- 1 x PEG: DI(HYDROXYETHYL)ETHER(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 HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.54: 20 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, Q.53
22 PLIP interactions:9 interactions with chain D, 3 interactions with chain B, 10 interactions with chain C,- Hydrophobic interactions: D:L.20, D:L.24, D:L.43, D:L.51, C:L.49, C:L.49, C:T.99, C:H.105
- Hydrogen bonds: D:G.50
- Water bridges: D:R.14, D:R.14, B:H.216, B:T.217, 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.55: 13 residues within 4Å:- Chain B: R.223
- Chain C: K.31, W.32, S.33, L.34, P.35, A.37, M.38, T.41, F.93, Y.97, E.120
- Ligands: UNL.62
11 PLIP interactions:8 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:L.34, C:A.37, C:F.93, C:Y.97
- Hydrogen bonds: C:K.31, C:K.31, C:L.34, C:E.120, B:R.223
- Water bridges: B:R.223
- Salt bridges: B:R.223
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.76: 16 residues within 4Å:- Chain C: L.49, G.52, V.53, L.91, I.137, M.140
- Chain D: L.24, A.27, Y.28, L.39, C.94, V.97, A.98, W.101
- Ligands: UNL.57, UNL.66
12 PLIP interactions:5 interactions with chain C, 7 interactions with chain D- Hydrophobic interactions: C:L.49, C:V.53, C:L.91, C:I.137, D:L.24, D:A.27, D:L.39, D:W.101, D:W.101
- Hydrogen bonds: C:M.140, D:Y.28, D:Y.28
- 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 1.97 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)
- 1 x OAA: OXALOACETATE ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 80 x UNL: UNKNOWN LIGAND(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(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 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.