- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.27 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)
- 59 x UNL: UNKNOWN LIGAND
UNL.4: 1 residues within 4Å:- Chain A: H.505
Ligand excluded by PLIPUNL.6: 8 residues within 4Å:- Chain A: K.49, L.50, T.228, W.515, T.517, E.524
- Chain B: R.63
- Ligands: UNL.20
Ligand excluded by PLIPUNL.7: 1 residues within 4Å:- Chain A: F.137
Ligand excluded by PLIPUNL.8: 5 residues within 4Å:- Chain A: R.218, H.227, A.260
- Chain B: R.66
- Ligands: UNL.12
Ligand excluded by PLIPUNL.9: 3 residues within 4Å:- Chain A: A.334, P.338
- Chain B: E.157
Ligand excluded by PLIPUNL.10: 4 residues within 4Å:- Chain A: R.580, P.600, V.601, D.603
Ligand excluded by PLIPUNL.11: 5 residues within 4Å:- Chain A: S.497, R.501, Y.537, G.592, K.593
Ligand excluded by PLIPUNL.12: 6 residues within 4Å:- Chain A: F.221, S.222, G.259, A.260, G.261
- 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: 7 residues within 4Å:- Chain A: E.175, E.197
- Chain B: R.62, V.108, D.114, S.116
- Chain C: K.15
Ligand excluded by PLIPUNL.16: 2 residues within 4Å:- Chain A: Y.586, K.597
Ligand excluded by PLIPUNL.17: 2 residues within 4Å:- Chain A: W.78, 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: 8 residues within 4Å:- Chain A: L.50, F.51, R.54, E.175, W.515
- Chain B: R.62
- Ligands: UNL.6, UNL.35
Ligand excluded by PLIPUNL.21: 2 residues within 4Å:- Chain A: G.339, T.343
Ligand excluded by PLIPUNL.22: 2 residues within 4Å:- Chain A: N.75, W.76
Ligand excluded by PLIPUNL.23: 3 residues within 4Å:- Chain A: H.56, S.229
- Ligands: FAD.1
Ligand excluded by PLIPUNL.24: 6 residues within 4Å:- Chain A: N.65, F.130, G.131, Q.133, L.409, G.410
Ligand excluded by PLIPUNL.25: 5 residues within 4Å:- Chain A: G.27, A.29, G.30, A.212
- Ligands: FAD.1
Ligand excluded by PLIPUNL.26: 4 residues within 4Å:- Chain A: N.208, Y.393, T.431, C.432
Ligand excluded by PLIPUNL.27: 5 residues within 4Å:- Chain A: R.128, A.129, H.144, G.270
- Ligands: UNL.28
Ligand excluded by PLIPUNL.28: 4 residues within 4Å:- Chain A: G.270, E.271, G.272
- Ligands: UNL.27
Ligand excluded by PLIPUNL.32: 5 residues within 4Å:- Chain B: H.104, M.105, G.175
- Chain C: F.12, W.13
Ligand excluded by PLIPUNL.33: 3 residues within 4Å:- Chain B: K.151, I.192, S.194
Ligand excluded by PLIPUNL.34: 4 residues within 4Å:- Chain B: I.125, E.126, K.130, Q.205
Ligand excluded by PLIPUNL.35: 6 residues within 4Å:- Chain A: F.51, R.54, E.175
- Chain B: R.62, Y.119
- Ligands: UNL.20
Ligand excluded by PLIPUNL.36: 4 residues within 4Å:- Chain B: Q.150, K.151, D.153
- Ligands: UNL.42
Ligand excluded by PLIPUNL.37: 1 residues within 4Å:- Chain B: D.176
Ligand excluded by PLIPUNL.38: 2 residues within 4Å:- Chain B: M.30
- Chain C: P.25
Ligand excluded by PLIPUNL.39: 2 residues within 4Å:- Chain B: S.124, E.126
Ligand excluded by PLIPUNL.40: 5 residues within 4Å:- Chain A: F.347
- Chain B: M.43, D.46, R.66, C.85
Ligand excluded by PLIPUNL.41: 3 residues within 4Å:- Chain B: C.40, G.41, D.46
Ligand excluded by PLIPUNL.42: 7 residues within 4Å:- Chain B: G.154, L.155, Y.188, N.230, K.233, A.234
- Ligands: UNL.36
Ligand excluded by PLIPUNL.43: 4 residues within 4Å:- Chain A: S.466
- Chain B: K.52, N.53, S.57
Ligand excluded by PLIPUNL.44: 3 residues within 4Å:- Chain B: C.215, T.217, K.239
Ligand excluded by PLIPUNL.45: 2 residues within 4Å:- Chain B: T.86, P.226
Ligand excluded by PLIPUNL.46: 6 residues within 4Å:- Chain B: P.103, H.104, M.105, T.166, Y.171, W.172
Ligand excluded by PLIPUNL.47: 5 residues within 4Å:- Chain B: Q.144, D.148, I.192, D.193, S.194
Ligand excluded by PLIPUNL.48: 3 residues within 4Å:- Chain B: M.191, R.202, Q.205
Ligand excluded by PLIPUNL.49: 1 residues within 4Å:- Chain B: C.40
Ligand excluded by PLIPUNL.50: 1 residues within 4Å:- Chain B: Q.150
Ligand excluded by PLIPUNL.54: 2 residues within 4Å:- Chain A: Y.162
- Chain C: E.8
Ligand excluded by PLIPUNL.55: 6 residues within 4Å:- Chain C: S.50, S.54
- Chain D: G.47, H.48, S.76, T.79
Ligand excluded by PLIPUNL.56: 8 residues within 4Å:- Chain C: V.53, F.56, A.87, L.91
- Chain D: L.43, I.93, L.100
- Ligands: 3PE.63
Ligand excluded by PLIPUNL.57: 5 residues within 4Å:- Chain C: L.95, T.99, W.100, I.137
- Chain D: L.21
Ligand excluded by PLIPUNL.58: 3 residues within 4Å:- Chain C: G.44, T.45, A.48
Ligand excluded by PLIPUNL.59: 3 residues within 4Å:- Chain C: T.4, A.5, K.6
Ligand excluded by PLIPUNL.60: 5 residues within 4Å:- Chain C: Y.30, K.31, W.32, A.37
- Ligands: UMQ.53
Ligand excluded by PLIPUNL.61: 4 residues within 4Å:- Chain C: A.59, A.60, E.65, F.67
Ligand excluded by PLIPUNL.62: 2 residues within 4Å:- Chain C: A.72, S.76
Ligand excluded by PLIPUNL.64: 4 residues within 4Å:- Chain D: H.9, H.48, W.49, Y.73
Ligand excluded by PLIPUNL.65: 3 residues within 4Å:- Chain D: A.41, T.44, F.80
Ligand excluded by PLIPUNL.66: 3 residues within 4Å:- Chain D: A.34, S.38
- Ligands: UNL.67
Ligand excluded by PLIPUNL.67: 6 residues within 4Å:- Chain D: G.32, P.33, A.34, Y.37
- Ligands: UNL.66, UNL.68
Ligand excluded by PLIPUNL.68: 5 residues within 4Å:- Chain D: P.33, Y.37, Y.88
- Ligands: UNL.67, UNL.69
Ligand excluded by PLIPUNL.69: 3 residues within 4Å:- Chain D: Y.88, Y.89
- Ligands: UNL.68
Ligand excluded by PLIPUNL.70: 4 residues within 4Å:- Chain D: D.36, N.87, V.91, G.92
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 AT5: 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE(Non-covalent)
AT5.51: 16 residues within 4Å:- Chain B: P.169, S.170, W.172, W.173, H.216, I.218
- Chain C: H.26, I.27, W.32, M.36, S.39, I.40, R.43
- Chain D: D.57, Y.58
- Ligands: HEM.52
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:W.32, C:I.40, B:W.173
- Hydrogen bonds: C:S.39
- Halogen bonds: C:H.26
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.52: 21 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.21, L.24, L.43, H.46, G.50, V.54
- Ligands: AT5.51
14 PLIP interactions:6 interactions with chain C, 7 interactions with chain D, 1 interactions with chain B,- Hydrophobic interactions: C:L.49, C:H.105, D:L.20, D:L.21, D:L.24, D:L.43
- 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
- 1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
UMQ.53: 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, E.120
- Ligands: UNL.60
10 PLIP interactions:8 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:A.37, C:T.41, C:F.93
- Hydrogen bonds: C:K.31, C:K.31, C:K.31, C:L.34, C:E.120, B:R.223
- Salt bridges: B:R.223
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.63: 13 residues within 4Å:- Chain C: L.49, G.52, L.91, L.95, I.137, M.140
- Chain D: A.27, Y.28, L.43, C.94, V.97, W.101
- Ligands: UNL.56
8 PLIP interactions:5 interactions with chain D, 3 interactions with chain C- Hydrophobic interactions: D:L.43, D:V.97, D:W.101, D:W.101, D:W.101, C:L.49, C:L.91, C:I.137
- 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 2.27 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)
- 59 x UNL: UNKNOWN LIGAND
- 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 AT5: 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE(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.