- 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 Y3P: (~{Z})-2-oxidanylbut-2-enedioic acid(Non-covalent)
Y3P.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
12 PLIP interactions:12 interactions with chain A- Hydrophobic interactions: A:F.130
- Hydrogen bonds: A:G.62, A:H.253, 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
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:N.366, A:M.367, A:E.397, A:A.399
K.30: 5 residues within 4Å:- Chain B: M.191, D.193, D.196, T.199
- Ligands: UNL.32
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.193, B:T.199, H2O.10
- 65 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)
UNL.4: 3 residues within 4Å:- Chain A: 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: 3 residues within 4Å:- Chain A: 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.41
Ligand excluded by PLIPUNL.9: 4 residues within 4Å:- Chain A: R.152, A.334, P.338
- Chain B: E.157
Ligand excluded by PLIPUNL.10: 6 residues within 4Å:- Chain A: E.560, H.578, R.580, P.600, V.601
- Ligands: UNL.25
Ligand excluded by PLIPUNL.12: 3 residues within 4Å:- Chain A: F.221, G.259
- Ligands: UNL.8
Ligand excluded by PLIPUNL.13: 7 residues within 4Å:- Chain A: M.367, A.399, S.400, A.401, S.402, V.403, H.404
Ligand excluded by PLIPUNL.14: 6 residues within 4Å:- Chain A: E.197
- Chain B: R.62, V.108, D.114, S.116
- Chain C: K.15
Ligand excluded by PLIPUNL.15: 1 residues within 4Å:- Chain A: Y.586
Ligand excluded by PLIPUNL.16: 3 residues within 4Å:- Chain A: D.73, L.135, Q.136
Ligand excluded by PLIPUNL.17: 3 residues within 4Å:- Chain A: W.78, Q.136, F.137
Ligand excluded by PLIPUNL.18: 5 residues within 4Å:- Chain A: R.557, D.559, F.561, D.562, Y.563
Ligand excluded by PLIPUNL.19: 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.20: 7 residues within 4Å:- Chain A: L.50, F.51, R.54, E.175
- Chain B: R.62, S.72
- Ligands: UNL.34
Ligand excluded by PLIPUNL.21: 2 residues within 4Å:- Chain A: Q.11, D.454
Ligand excluded by PLIPUNL.22: 1 residues within 4Å:- Chain A: T.462
Ligand excluded by PLIPUNL.23: 2 residues within 4Å:- Chain A: R.32, R.422
Ligand excluded by PLIPUNL.24: 1 residues within 4Å:- Chain A: N.383
Ligand excluded by PLIPUNL.25: 3 residues within 4Å:- Chain A: F.575, H.578
- Ligands: UNL.10
Ligand excluded by PLIPUNL.26: 3 residues within 4Å:- Chain A: E.608, S.612, S.613
Ligand excluded by PLIPUNL.31: 6 residues within 4Å:- Chain B: H.104, M.105, Y.106, Y.171
- Chain C: F.12, W.13
Ligand excluded by PLIPUNL.32: 3 residues within 4Å:- Chain B: I.192, S.194
- Ligands: K.30
Ligand excluded by PLIPUNL.33: 6 residues within 4Å:- Chain B: I.125, E.126, K.130, E.201, R.202, Q.205
Ligand excluded by PLIPUNL.34: 7 residues within 4Å:- Chain A: F.51, R.54, E.175
- Chain B: R.62, L.115, Y.119
- Ligands: UNL.20
Ligand excluded by PLIPUNL.35: 2 residues within 4Å:- Chain B: Q.150, K.151
Ligand excluded by PLIPUNL.36: 5 residues within 4Å:- Chain B: D.153, L.155, Y.188, N.230, A.234
Ligand excluded by PLIPUNL.37: 4 residues within 4Å:- Chain B: Y.17, M.30, Y.100
- Chain C: P.25
Ligand excluded by PLIPUNL.38: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.39: 5 residues within 4Å:- Chain B: C.40, G.41, D.46, I.49, K.50
Ligand excluded by PLIPUNL.40: 1 residues within 4Å:- Chain B: S.9
Ligand excluded by PLIPUNL.41: 3 residues within 4Å:- Chain A: A.260
- Chain B: R.66
- Ligands: UNL.8
Ligand excluded by PLIPUNL.42: 2 residues within 4Å:- Chain B: H.104, W.173
Ligand excluded by PLIPUNL.43: 4 residues within 4Å:- Chain B: E.67, G.68, I.69, K.227
Ligand excluded by PLIPUNL.44: 2 residues within 4Å:- Chain B: N.230
- Ligands: UNL.61
Ligand excluded by PLIPUNL.45: 3 residues within 4Å:- Chain A: N.112
- Chain B: Q.137, Y.142
Ligand excluded by PLIPUNL.49: 2 residues within 4Å:- Chain A: Y.162
- Chain C: E.8
Ligand excluded by PLIPUNL.50: 6 residues within 4Å:- Chain C: S.50, S.54
- Chain D: T.44, H.48, S.76, T.79
Ligand excluded by PLIPUNL.51: 7 residues within 4Å:- Chain C: V.53, F.56, L.91
- Chain D: L.43, I.93, L.100
- Ligands: 3PE.68
Ligand excluded by PLIPUNL.52: 5 residues within 4Å:- Chain C: S.96, T.99, W.100
- Chain D: L.21, G.22
Ligand excluded by PLIPUNL.53: 1 residues within 4Å:- Chain C: G.44
Ligand excluded by PLIPUNL.54: 3 residues within 4Å:- Chain C: T.4, A.5, K.6
Ligand excluded by PLIPUNL.55: 2 residues within 4Å:- Chain B: D.176
- Chain C: W.13
Ligand excluded by PLIPUNL.56: 4 residues within 4Å:- Chain C: W.32, A.37, I.40
- Ligands: UMQ.48
Ligand excluded by PLIPUNL.57: 5 residues within 4Å:- Chain C: F.56, A.59, E.65, F.67
- Chain D: F.86
Ligand excluded by PLIPUNL.58: 1 residues within 4Å:- Chain C: A.87
Ligand excluded by PLIPUNL.59: 2 residues within 4Å:- Chain C: W.100, V.126
Ligand excluded by PLIPUNL.60: 4 residues within 4Å:- Chain C: K.112, G.113, Q.118
- Ligands: UNL.65
Ligand excluded by PLIPUNL.61: 4 residues within 4Å:- Chain B: T.222
- Chain C: K.115, L.116
- Ligands: UNL.44
Ligand excluded by PLIPUNL.62: 3 residues within 4Å:- Chain C: Q.66, P.68
- Chain D: D.90
Ligand excluded by PLIPUNL.63: 5 residues within 4Å:- Chain B: S.116
- Chain C: E.8, R.11, F.12, K.15
Ligand excluded by PLIPUNL.64: 1 residues within 4Å:- Chain C: V.47
Ligand excluded by PLIPUNL.65: 5 residues within 4Å:- Chain C: G.113, F.114, K.115, Q.118
- Ligands: UNL.60
Ligand excluded by PLIPUNL.66: 1 residues within 4Å:- Ligands: 3PE.68
Ligand excluded by PLIPUNL.67: 2 residues within 4Å:- Chain B: W.173
- Chain C: H.26
Ligand excluded by PLIPUNL.69: 6 residues within 4Å:- Chain D: H.9, H.48, W.49, N.69, L.72, Y.73
Ligand excluded by PLIPUNL.70: 3 residues within 4Å:- Chain D: A.41, T.44, F.80
Ligand excluded by PLIPUNL.71: 1 residues within 4Å:- Chain D: A.42
Ligand excluded by PLIPUNL.72: 4 residues within 4Å:- Chain D: A.34, Y.37, S.38
- Ligands: UNL.73
Ligand excluded by PLIPUNL.73: 4 residues within 4Å:- Chain D: P.33, A.34
- Ligands: UNL.72, UNL.74
Ligand excluded by PLIPUNL.74: 5 residues within 4Å:- Chain D: Y.37, F.80, C.84, Y.88
- Ligands: UNL.73
Ligand excluded by PLIPUNL.75: 3 residues within 4Å:- Chain D: Y.85, Y.88, Y.89
Ligand excluded by PLIPUNL.76: 2 residues within 4Å:- Chain D: Y.58, H.60
Ligand excluded by PLIPUNL.77: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.78: 2 residues within 4Å:- Chain C: Q.66
- Chain D: Y.85
Ligand excluded by PLIP- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x MOH: METHANOL(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.46: 18 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, L.20, L.43, H.46, G.50, L.51, Q.53
21 PLIP interactions:9 interactions with chain C, 10 interactions with chain D, 2 interactions with chain B,- Hydrophobic interactions: C:L.49, C:L.49, C:T.99, C:H.105, D:L.20, D:L.43, D:L.51
- Water bridges: C:H.105, D:R.14, D:R.14, D:R.14, B:T.217
- Salt bridges: C:R.43, C:H.105, D:R.14, B:H.216
- pi-Stacking: C:H.42
- Metal complexes: C:H.98, D:H.46
- Hydrogen bonds: D:G.50
- pi-Cation interactions: D:H.46
- 1 x 9AU: 4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one(Non-covalent)
- 1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
UMQ.48: 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.56
10 PLIP interactions:9 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:L.34, C:A.37, C:T.41, C:F.93, C:Y.97
- Hydrogen bonds: C:K.31, C:L.34, C:E.120, B:R.223
- Water bridges: C:E.120
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.68: 17 residues within 4Å:- Chain C: L.49, G.52, V.53, L.91, L.95, I.137, M.140
- Chain D: L.24, A.27, Y.28, L.39, C.94, V.97, A.98, W.101
- Ligands: UNL.51, UNL.66
11 PLIP interactions:6 interactions with chain D, 5 interactions with chain C- Hydrophobic interactions: D:L.24, D:A.27, D:L.39, D:W.101, D:W.101, C:L.49, C:V.53, C:L.91, C:L.95, C:I.137
- Hydrogen bonds: 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 Y3P: (~{Z})-2-oxidanylbut-2-enedioic acid(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 65 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 1 x MOH: METHANOL(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 9AU: 4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one(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.