- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 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
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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 43 x UNL: UNKNOWN LIGAND(Non-functional Binders)
UNL.5: 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.6: 8 residues within 4Å:- Chain A: Y.162, L.166, Y.172, V.174
- Chain B: S.116, Y.119, K.123
- Chain C: E.8
Ligand excluded by PLIPUNL.7: 3 residues within 4Å:- Chain A: R.557, D.559, Y.563
Ligand excluded by PLIPUNL.8: 2 residues within 4Å:- Chain A: F.137, S.612
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, K.572, H.578, R.580, P.600, V.601
Ligand excluded by PLIPUNL.11: 7 residues within 4Å:- Chain A: Y.98, Y.374, K.375, A.423, L.426, T.427, E.430
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: 5 residues within 4Å:- Chain A: P.330, L.333, A.334, S.341, T.353
Ligand excluded by PLIPUNL.14: 8 residues within 4Å:- Chain A: A.212, T.213, G.214, C.395, G.396, E.397, A.398
- Ligands: FAD.1
Ligand excluded by PLIPUNL.15: 4 residues within 4Å:- Chain A: H.56, S.225, S.229
- Ligands: FAD.1
Ligand excluded by PLIPUNL.16: 4 residues within 4Å:- Chain A: R.167
- Chain B: K.130, K.131, E.134
Ligand excluded by PLIPUNL.17: 4 residues within 4Å:- Chain A: W.76, R.77, E.101, D.610
Ligand excluded by PLIPUNL.18: 2 residues within 4Å:- Chain A: R.457, I.513
Ligand excluded by PLIPUNL.19: 3 residues within 4Å:- Chain A: I.602, D.603, R.604
Ligand excluded by PLIPUNL.23: 5 residues within 4Å:- Chain A: R.218, F.221, C.223, A.260
- Chain B: R.66
Ligand excluded by PLIPUNL.24: 2 residues within 4Å:- Chain B: D.176
- Chain C: W.13
Ligand excluded by PLIPUNL.25: 5 residues within 4Å:- Chain B: H.104, M.105, Y.106
- Chain C: F.12, W.13
Ligand excluded by PLIPUNL.26: 4 residues within 4Å:- Chain B: W.173
- Ligands: UNL.28, BOG.43, UNL.46
Ligand excluded by PLIPUNL.27: 6 residues within 4Å:- Chain A: F.51, R.54, E.175
- Chain B: R.62, L.115, Y.119
Ligand excluded by PLIPUNL.28: 2 residues within 4Å:- Chain C: I.27
- Ligands: UNL.26
Ligand excluded by PLIPUNL.29: 4 residues within 4Å:- Chain B: N.230, K.233
- Chain C: K.115, L.116
Ligand excluded by PLIPUNL.30: 4 residues within 4Å:- Chain B: I.125, E.126, K.130, Q.205
Ligand excluded by PLIPUNL.31: 6 residues within 4Å:- Chain A: N.112, R.164
- Chain B: L.129, E.134, Q.137, Y.142
Ligand excluded by PLIPUNL.32: 3 residues within 4Å:- Chain B: Q.205, Q.207, D.208
Ligand excluded by PLIPUNL.33: 4 residues within 4Å:- Chain B: I.77, G.80, T.82, K.87
Ligand excluded by PLIPUNL.34: 3 residues within 4Å:- Chain B: Y.213
- Chain D: Q.53
- Ligands: UNL.53
Ligand excluded by PLIPUNL.38: 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.39: 2 residues within 4Å:- Chain C: F.56
- Ligands: 3PE.44
Ligand excluded by PLIPUNL.40: 3 residues within 4Å:- Chain C: S.96, W.100
- Ligands: UNL.47
Ligand excluded by PLIPUNL.41: 2 residues within 4Å:- Chain C: I.27, W.32
Ligand excluded by PLIPUNL.42: 6 residues within 4Å:- Chain B: Y.100, P.101, P.103
- Chain C: S.24, P.25, I.29
Ligand excluded by PLIPUNL.45: 4 residues within 4Å:- Chain D: H.9, S.12, H.48, W.49
Ligand excluded by PLIPUNL.46: 4 residues within 4Å:- Chain C: I.40
- Chain D: Y.58
- Ligands: UNL.26, BOG.43
Ligand excluded by PLIPUNL.47: 3 residues within 4Å:- Chain D: L.21, P.25
- Ligands: UNL.40
Ligand excluded by PLIPUNL.48: 5 residues within 4Å:- Chain B: F.210
- Chain D: I.55, T.56, V.59, I.65
Ligand excluded by PLIPUNL.49: 4 residues within 4Å:- Chain D: A.34, S.38, A.41
- Ligands: UNL.50
Ligand excluded by PLIPUNL.50: 5 residues within 4Å:- Chain D: P.33, A.34, Y.37
- Ligands: UNL.49, UNL.51
Ligand excluded by PLIPUNL.51: 4 residues within 4Å:- Chain D: Y.37, Y.88
- Ligands: UNL.50, UNL.52
Ligand excluded by PLIPUNL.52: 4 residues within 4Å:- Chain D: Y.88, Y.89
- Ligands: UNL.51, UNL.55
Ligand excluded by PLIPUNL.53: 8 residues within 4Å:- Chain B: Y.213, R.214
- Chain D: A.6, H.9, W.10, E.13, Q.53
- Ligands: UNL.34
Ligand excluded by PLIPUNL.54: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.55: 1 residues within 4Å:- Ligands: UNL.52
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 K7G: thiapronil(Non-covalent)
K7G.35: 14 residues within 4Å:- Chain B: P.169, S.170, W.172, W.173, H.216, I.218
- Chain C: I.27, Y.30, W.32, M.36, S.39, I.40, R.43
- Chain D: Y.58
6 PLIP interactions:3 interactions with chain B, 3 interactions with chain C- Hydrophobic interactions: B:P.169, B:W.172, B:H.216, C:Y.30, C:I.40
- pi-Cation interactions: C:R.43
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.36: 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, L.106
- Chain D: R.14, L.20, L.24, L.43, H.46, G.50, L.51
19 PLIP interactions:9 interactions with chain C, 9 interactions with chain D, 1 interactions with chain B,- Hydrophobic interactions: C:L.49, C:L.49, C:H.105, C:L.106, D:L.20, D:L.24, D:L.43, D:L.51
- Water bridges: C:H.105, D:R.14, D:R.14
- 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.37: 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, L.116, E.120
9 PLIP interactions:6 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:A.37, C:T.41, C:F.93
- Hydrogen bonds: C:K.31, C:L.34, C:E.120, B:R.223, B:R.223
- Salt bridges: B:R.223
- 1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.44: 12 residues within 4Å:- Chain C: L.49, V.53, L.91, I.137, M.140
- Chain D: A.27, Y.28, C.94, V.97, A.98, W.101
- Ligands: UNL.39
7 PLIP interactions:3 interactions with chain C, 4 interactions with chain D- Hydrophobic interactions: C:L.49, C:V.53, C:I.137, D:A.27, D:V.97, D:V.97
- 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
- 2019-10-16
- 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 2.15 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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 43 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 K7G: thiapronil(Non-covalent)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)
- 1 x BOG: octyl beta-D-glucopyranoside(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
- 2019-10-16
- 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.