- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 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 MN: MANGANESE (II) ION(Non-covalent)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 49 x UNL: UNKNOWN LIGAND(Non-functional Binders)
UNL.6: 8 residues within 4Å:- Chain A: K.49, T.228, W.515, T.517, V.520, E.521, E.524
- Chain B: R.63
Ligand excluded by PLIPUNL.7: 3 residues within 4Å:- Chain A: Y.162
- Chain B: K.123
- Chain C: E.8
Ligand excluded by PLIPUNL.8: 6 residues within 4Å:- Chain A: R.557, D.559, F.561, D.562, Y.563, S.564
Ligand excluded by PLIPUNL.9: 3 residues within 4Å:- Chain A: F.137, S.612, V.614
Ligand excluded by PLIPUNL.10: 5 residues within 4Å:- Chain A: R.218, H.227, A.260
- Chain B: R.66
- Ligands: UNL.15
Ligand excluded by PLIPUNL.11: 4 residues within 4Å:- Chain A: R.152, A.334, P.338
- Chain B: E.157
Ligand excluded by PLIPUNL.12: 6 residues within 4Å:- Chain A: E.560, K.572, H.578, R.580, P.600, V.601
Ligand excluded by PLIPUNL.13: 3 residues within 4Å:- Chain A: K.375, T.427, E.430
Ligand excluded by PLIPUNL.14: 6 residues within 4Å:- Chain A: L.50, F.51, R.54, E.175
- Chain B: S.72
- Ligands: UNL.30
Ligand excluded by PLIPUNL.15: 3 residues within 4Å:- Chain A: F.221, G.259
- Ligands: UNL.10
Ligand excluded by PLIPUNL.16: 7 residues within 4Å:- Chain A: R.464, T.465, S.466, K.507, T.508, D.518
- Chain B: S.57
Ligand excluded by PLIPUNL.17: 3 residues within 4Å:- Chain A: E.184, N.185, R.189
Ligand excluded by PLIPUNL.18: 4 residues within 4Å:- Chain A: E.122, K.124
- Chain B: L.143
- Ligands: UNL.38
Ligand excluded by PLIPUNL.19: 4 residues within 4Å:- Chain A: L.68, G.69, N.70, K.124
Ligand excluded by PLIPUNL.20: 2 residues within 4Å:- Chain A: T.10, V.450
Ligand excluded by PLIPUNL.21: 3 residues within 4Å:- Chain A: G.36, E.39
- Ligands: UNL.22
Ligand excluded by PLIPUNL.22: 3 residues within 4Å:- Chain A: R.32, R.422
- Ligands: UNL.21
Ligand excluded by PLIPUNL.23: 3 residues within 4Å:- Chain A: D.88, R.557, R.619
Ligand excluded by PLIPUNL.24: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.25: 3 residues within 4Å:- Chain A: W.76, E.101, D.610
Ligand excluded by PLIPUNL.29: 5 residues within 4Å:- Chain B: H.104, M.105, Y.106
- Chain C: F.12, W.13
Ligand excluded by PLIPUNL.30: 6 residues within 4Å:- Chain A: F.51, R.54, E.175
- Chain B: R.62, Y.119
- Ligands: UNL.14
Ligand excluded by PLIPUNL.31: 3 residues within 4Å:- Chain B: K.151, I.192, S.194
Ligand excluded by PLIPUNL.32: 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.33: 6 residues within 4Å:- Chain B: I.125, E.126, K.130, E.201, R.202, Q.205
Ligand excluded by PLIPUNL.34: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.35: 5 residues within 4Å:- Chain B: E.140, Q.141, Y.142
- Ligands: UNL.36, UNL.38
Ligand excluded by PLIPUNL.36: 3 residues within 4Å:- Chain B: E.140, Y.142
- Ligands: UNL.35
Ligand excluded by PLIPUNL.37: 3 residues within 4Å:- Chain A: I.108
- Chain B: E.140, Q.141
Ligand excluded by PLIPUNL.38: 3 residues within 4Å:- Chain B: E.140
- Ligands: UNL.18, UNL.35
Ligand excluded by PLIPUNL.42: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.43: 2 residues within 4Å:- Chain D: L.43
- Ligands: 3PE.47
Ligand excluded by PLIPUNL.44: 6 residues within 4Å:- Chain C: S.96, T.99, W.100, I.137
- Chain D: L.21, P.25
Ligand excluded by PLIPUNL.45: 3 residues within 4Å:- Chain C: W.32, A.37
- Ligands: FTN.39
Ligand excluded by PLIPUNL.46: 4 residues within 4Å:- Chain C: G.113, F.114, K.115, Q.118
Ligand excluded by PLIPUNL.48: 5 residues within 4Å:- Chain D: H.9, H.48, W.49, Y.73
- Ligands: UNL.56
Ligand excluded by PLIPUNL.49: 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.50: 3 residues within 4Å:- Chain D: L.19, S.38
- Ligands: UNL.51
Ligand excluded by PLIPUNL.51: 4 residues within 4Å:- Chain D: L.19, A.41, A.42
- Ligands: UNL.50
Ligand excluded by PLIPUNL.52: 3 residues within 4Å:- Chain D: A.34, Y.37, S.38
Ligand excluded by PLIPUNL.53: 4 residues within 4Å:- Chain D: P.33, A.34, Y.37
- Ligands: UNL.54
Ligand excluded by PLIPUNL.54: 4 residues within 4Å:- Chain D: P.33, Y.37, Y.88
- Ligands: UNL.53
Ligand excluded by PLIPUNL.55: 3 residues within 4Å:- Chain D: Y.85, Y.88, Y.89
Ligand excluded by PLIPUNL.56: 2 residues within 4Å:- Ligands: UNL.48, UNL.58
Ligand excluded by PLIPUNL.57: 1 residues within 4Å:- Chain D: P.25
Ligand excluded by PLIPUNL.58: 3 residues within 4Å:- Chain D: H.9, W.49
- Ligands: UNL.56
Ligand excluded by PLIPUNL.59: 6 residues within 4Å:- Chain D: D.36, V.91, G.92, I.93, C.94, K.95
Ligand excluded by PLIPUNL.60: 2 residues within 4Å:- Chain D: W.10
- Ligands: UNL.61
Ligand excluded by PLIPUNL.61: 1 residues within 4Å:- Ligands: UNL.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 FTN: N-[3-(1-methylethoxy)phenyl]-2-(trifluoromethyl)benzamide(Non-covalent)
FTN.39: 14 residues within 4Å:- Chain B: P.169, S.170, W.173, H.216, I.218
- Chain C: I.27, W.32, M.36, S.39, I.40, R.43
- Chain D: D.57, Y.58
- Ligands: UNL.45
8 PLIP interactions:4 interactions with chain B, 4 interactions with chain C- Hydrophobic interactions: B:P.169, B:W.173, B:H.216, B:I.218, C:I.27, C:I.40, C:R.43
- pi-Cation interactions: C:R.43
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)
HEM.40: 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.24, L.43, H.46, G.50, L.51
20 PLIP interactions:10 interactions with chain D, 9 interactions with chain C, 1 interactions with chain B,- 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, C:R.43, C:H.105, B:H.216
- Metal complexes: D:H.46, C:H.98
- pi-Stacking: C:H.42
- 1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
UMQ.41: 11 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, Y.97, E.120
13 PLIP interactions:10 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, C:E.120, B:R.223, B:R.223
- Water bridges: C:L.116
- Salt bridges: B:R.223
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.47: 15 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, P.31, C.94, V.97, A.98, W.101
- Ligands: UNL.43
10 PLIP interactions:5 interactions with chain C, 5 interactions with chain D- Hydrophobic interactions: C:L.49, C:V.53, C:L.91, C:L.91, C:I.137, D:L.24, D:Y.28, D:V.97, D:W.101
- 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 2.20 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 MN: MANGANESE (II) ION(Non-covalent)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 49 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 FTN: N-[3-(1-methylethoxy)phenyl]-2-(trifluoromethyl)benzamide(Non-covalent)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(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.