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Crystal structure of mitochondrial rhodoquinol-fumarate reductase from ascaris suum with N-[(2,4-DICHLOROPHENYL)METHYL]-2-(trifluoromethyl) benzamide
Analyse Crystal structure of mitochondrial rhodoquinol-fumarate reductase from ascaris… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YSY
- Type
- protein
- Length
- 2,296 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase flavoprotein; Succinate dehydrogenase [ubiquinone] iron-sulfur…
- EC
- 1.3.5.1
- UniProt
- U1LRQ3, O44074, P92506, P92507
- Ligands
- FAD, FES, SF4, F3S, E24, HEM, EPH
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Succinate dehydrogenase flavoprotein | protein | 616 | 33% helix, 22% strand | U1LRQ3 |
| B, F | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1) | protein | 250 | 28% helix, 15% strand | O44074 |
| C, G | Cytochrome B-large subunit | protein | 153 | 75% helix, 1% strand | P92506 |
| D, H | Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial | protein | 129 | 67% helix, 2% strand | P92507 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, E
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, F
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, F
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, F
- E24 · N-(2,4-dichlorobenzyl)-2-(trifluoromethyl)benzamide · ligand · 2 copies · chains B, C, D, F, G, H
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C, D, F, G, H
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · 2 copies · chains C, D, G, H
- MLI · Malonate ion · additive · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.86 | 0.86 | 96 | E24, HEM, EPH |
| 2 | 306 | 0.85 | 0.95 | 52 | MLI, FAD |
| 3 | 307 | 0.85 | 0.95 | 56 | MLI, FAD |
| 4 | 1176 | 0.85 | 0.85 | 93 | E24, HEM, EPH |
| 5 | 770 | 0.78 | 0.82 | 78 | empty |
Interfaces
17 interfaces between chains.
- E–F · 2792 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2772 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1932 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1926 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1839 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4YSY · Crystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with… · the same entry in another collection · chain H against H, TM-score 1.00
- P92507 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain H against A, TM-score 0.89
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 U1LRQ3
- Every structure of UniProt O44074
- Every structure of UniProt P92506
- Every structure of UniProt P92507
- Elsewhere: RCSB PDB 4YSY · PDBe 4YSY · UniProt U1LRQ3 · UniProt O44074 · UniProt P92506 · UniProt P92507
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