Research workbench
Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode ascaris suum with the specific inhibitor flutolanil
Analyse Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VR9
- Type
- protein
- Length
- 2,288 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavoprotein subunit of complex II; Iron-sulfur subunit of succinate dehydrogenase…
- UniProt
- Q33862, O44074, P92506, P92507
- Ligands
- FAD, FES, SF4, F3S, HEM, FTN, EPH
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Flavoprotein subunit of complex II | protein | 613 | 34% helix, 21% strand | Q33862 |
| B, F | Iron-sulfur subunit of succinate dehydrogenase | protein | 249 | 27% helix, 14% strand | O44074 |
| C, G | Cytochrome B-large subunit | protein | 153 | 65% helix, 1% strand | P92506 |
| D, H | Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial | protein | 129 | 71% helix, 2% strand | P92507 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, 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
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, C, D, F, G, H
- FTN · N-[3-(1-methylethoxy)phenyl]-2-(trifluoromethyl) benzamide · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.85 | 0.86 | 98 | HEM, FTN, EPH |
| 2 | 295 | 0.85 | 0.96 | 53 | MLI, FAD |
| 3 | 292 | 0.85 | 0.96 | 53 | MLI, FAD |
| 4 | 1132 | 0.85 | 0.85 | 102 | FTN, HEM, EPH |
| 5 | 819 | 0.80 | 0.83 | 94 | empty |
Interfaces
17 interfaces between chains.
- E–F · 2817 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 2810 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 1881 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1872 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1835 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 3VR9 · Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum… · the same entry in another collection · chain G against G, TM-score 1.00
- P92507 · AlphaFold monomer V2.0 prediction for succinate dehydrogenase [ubiquinone] cytochrome B… · a predicted model of the same protein · chain D against A, TM-score 0.89
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 Q33862
- Every structure of UniProt O44074
- Every structure of UniProt P92506
- Every structure of UniProt P92507
- Elsewhere: RCSB PDB 3VR9 · PDBe 3VR9 · UniProt Q33862 · UniProt O44074 · UniProt P92506 · UniProt P92507
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