- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.37 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- 1 x OAA: OXALOACETATE ION(Non-covalent)
OAA.3: 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
- 40 x UNL: UNKNOWN LIGAND(Non-functional Binders)
UNL.4: 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.5: 9 residues within 4Å:- Chain A: F.51, Y.162, L.166, Y.172, V.174
- Chain B: S.116, Y.119, K.123
- Chain C: E.8
Ligand excluded by PLIPUNL.6: 5 residues within 4Å:- Chain A: R.557, D.559, F.561, D.562, Y.563
Ligand excluded by PLIPUNL.7: 2 residues within 4Å:- Chain A: F.137, S.612
Ligand excluded by PLIPUNL.8: 5 residues within 4Å:- Chain A: R.152, A.334, P.338
- Chain B: Y.156, E.157
Ligand excluded by PLIPUNL.9: 4 residues within 4Å:- Chain A: E.560, R.580, P.600, V.601
Ligand excluded by PLIPUNL.10: 1 residues within 4Å:- Chain A: Y.98
Ligand excluded by PLIPUNL.11: 3 residues within 4Å:- Chain A: R.218, F.221
- Chain B: R.66
Ligand excluded by PLIPUNL.12: 1 residues within 4Å:- Chain A: T.10
Ligand excluded by PLIPUNL.13: 3 residues within 4Å:- Chain A: H.97, E.101, D.610
Ligand excluded by PLIPUNL.14: 5 residues within 4Å:- Chain A: G.36, E.39, R.422, A.425, L.426
Ligand excluded by PLIPUNL.15: 1 residues within 4Å:- Chain A: H.505
Ligand excluded by PLIPUNL.16: 5 residues within 4Å:- Chain A: Q.61, C.262, L.263, T.343
- Chain B: E.67
Ligand excluded by PLIPUNL.17: 7 residues within 4Å:- Chain A: R.54, S.55, H.56, A.226
- Chain B: S.64, C.65, C.70
Ligand excluded by PLIPUNL.21: 3 residues within 4Å:- Chain B: D.176, K.177
- Chain C: W.13
Ligand excluded by PLIPUNL.22: 5 residues within 4Å:- Chain B: H.104, M.105, Y.106
- Chain C: F.12, W.13
Ligand excluded by PLIPUNL.23: 3 residues within 4Å:- Chain B: K.151, I.192, S.194
Ligand excluded by PLIPUNL.24: 4 residues within 4Å:- Chain B: L.155, Y.188, N.230, A.234
Ligand excluded by PLIPUNL.25: 2 residues within 4Å:- Chain B: H.104, W.173
Ligand excluded by PLIPUNL.26: 2 residues within 4Å:- Chain B: R.202, Q.205
Ligand excluded by PLIPUNL.30: 5 residues within 4Å:- Chain C: W.100
- Chain D: A.18, L.21, G.22, P.25
Ligand excluded by PLIPUNL.31: 1 residues within 4Å:- Chain C: A.87
Ligand excluded by PLIPUNL.32: 3 residues within 4Å:- Chain C: K.112, G.113, Q.118
Ligand excluded by PLIPUNL.33: 1 residues within 4Å:- Chain C: V.126
Ligand excluded by PLIPUNL.34: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.35: 1 residues within 4Å:- Ligands: 3PE.36
Ligand excluded by PLIPUNL.37: 3 residues within 4Å:- Chain D: H.9, H.48, W.49
Ligand excluded by PLIPUNL.38: 7 residues within 4Å:- Chain C: S.50, S.54
- Chain D: T.44, G.47, H.48, L.51, S.76
Ligand excluded by PLIPUNL.39: 1 residues within 4Å:- Ligands: UNL.47
Ligand excluded by PLIPUNL.40: 4 residues within 4Å:- Chain D: E.13, S.17, H.46, W.49
Ligand excluded by PLIPUNL.41: 4 residues within 4Å:- Chain D: Y.37, S.38, A.41
- Ligands: UNL.42
Ligand excluded by PLIPUNL.42: 7 residues within 4Å:- Chain D: P.33, A.34, Y.37, F.80, C.84
- Ligands: UNL.41, UNL.43
Ligand excluded by PLIPUNL.43: 3 residues within 4Å:- Chain D: Y.37
- Ligands: UNL.42, UNL.44
Ligand excluded by PLIPUNL.44: 4 residues within 4Å:- Chain D: Y.85, Y.88, Y.89
- Ligands: UNL.43
Ligand excluded by PLIPUNL.45: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.46: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.47: 3 residues within 4Å:- Chain D: Y.58, H.60
- Ligands: UNL.39
Ligand excluded by PLIPUNL.48: 4 residues within 4Å:- Chain D: Y.58, V.59, H.60
- Ligands: UNL.49
Ligand excluded by PLIPUNL.49: 1 residues within 4Å:- Ligands: UNL.48
Ligand excluded by PLIPUNL.50: 0 residues within 4Å:- (No contacts)
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 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)
HEM.28: 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
- Chain D: R.14, S.17, L.20, L.43, H.46, G.50, L.51
- Ligands: AT5.27
16 PLIP interactions:9 interactions with chain C, 6 interactions with chain D, 1 interactions with chain B,- Hydrophobic interactions: C:L.49, C:T.99, C:H.105, D:L.20, D:L.43, D:L.51
- Water bridges: C:H.105, C:H.105
- 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.29: 10 residues within 4Å:- Chain B: R.223
- Chain C: W.32, S.33, L.34, P.35, A.37, M.38, T.41, E.120, L.127
8 PLIP interactions:5 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:T.41, C:L.127
- Hydrogen bonds: C:L.34, C:E.120, C:E.120, B:R.223, B:R.223
- Salt bridges: B:R.223
- 1 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)
3PE.36: 11 residues within 4Å:- Chain C: V.92, L.95, I.137, M.140
- Chain D: A.27, Y.28, C.94, V.97, A.98, W.101
- Ligands: UNL.35
10 PLIP interactions:4 interactions with chain C, 6 interactions with chain D- Hydrophobic interactions: C:V.92, C:L.95, C:I.137, D:A.27, D:V.97, D:V.97, D:W.101, D:W.101
- Hydrogen bonds: C:M.140, 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 2.37 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- 1 x OAA: OXALOACETATE ION(Non-covalent)
- 40 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 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.