MolNFT v1 · #57638 · protein
Crystal structure of porcine heart mitochondrial complex II bound with N-phenyl-2-(trifluoromethyl)-benzamide
3AE1 · Succinate dehydrogenase [ubiquinone] flavoprotein subunit…: “Crystal structure of porcine heart mitochondrial complex II bound with N-phenyl-2-(trifluoromethyl)-benzamide”. X-ray diffraction, 7 ligands (FAD, FES, SF4), 13 pockets…
- PDB
- 3AE1
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial; Succinate…
- EC
- 1.3.5.1
- UniProt
- Q0QF01, Q007T0, D0VWV4, A5GZW8
- Ligands
- FAD, FES, SF4, F3S, HEM, TFZ, EPH
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1) | protein | 613 | 34% helix, 21% strand | Q0QF01 |
| B | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1) | protein | 239 | 29% helix, 15% strand | Q007T0 |
| C | Succinate dehydrogenase cytochrome B560 subunit, mitochondrial | protein | 138 | 75% helix, 1% strand | D0VWV4 |
| D | Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial | protein | 102 | 86% helix, 0% strand | A5GZW8 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
- SF4 · Iron/sulfur cluster · ligand · chains B
- F3S · FE3-S4 cluster · ligand · chains B
- HEM · Protoporphyrin IX containing Fe · ligand · chains B, C, D
- TFZ · N-phenyl-2-(trifluoromethyl)benzamide · ligand · chains B, C, D
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains C, D
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.85 | 0.86 | 93 | HEM, TFZ, EPH |
| 2 | 322 | 0.85 | 0.95 | 55 | FAD, MLI |
| 3 | 83 | 0.74 | 0.97 | 21 | empty |
| 4 | 404 | 0.70 | 0.82 | 36 | empty |
| 5 | 529 | 0.70 | 0.79 | 56 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2796 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 1734 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1351 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 663 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 94 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 3AE1 · Crystal structure of porcine heart mitochondrial complex II bound with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q0QF01 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] flavoprotein… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q007T0 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] iron-sulfur… · a predicted model of the same protein · chain B against A, TM-score 0.99
- A5GZW8 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain D against A, TM-score 0.99
- D0VWV4 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase cytochrome B560 subunit… · a predicted model of the same protein · chain C against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q0QF01
- Every structure of UniProt Q007T0
- Every structure of UniProt D0VWV4
- Every structure of UniProt A5GZW8
- Elsewhere: RCSB PDB 3AE1 · PDBe 3AE1 · UniProt Q0QF01 · UniProt Q007T0 · UniProt D0VWV4 · UniProt A5GZW8
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