Research workbench
Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode ascaris suum
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
- 3VR8
- Type
- protein
- Length
- 2,285 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, RQX, EPH
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Flavoprotein subunit of complex II | protein | 613 | 35% helix, 22% strand | Q33862 |
| B, F | Iron-sulfur subunit of succinate dehydrogenase | protein | 249 | 32% helix, 14% strand | O44074 |
| C | Cytochrome B-large subunit | protein | 153 | 71% helix, 1% strand | P92506 |
| D, H | Succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial | protein | 129 | 69% helix, 1% strand | P92507 |
| G | Cytochrome B-large subunit | protein | 150 | 72% helix, 1% strand | P92506 |
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
- RQX · 2-amino-3-methoxy-6-methyl-5-[(2E)-3-methylhex-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione · 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 | 305 | 0.85 | 0.95 | 53 | MLI, FAD |
| 2 | 1123 | 0.85 | 0.85 | 90 | HEM, EPH |
| 3 | 302 | 0.84 | 0.95 | 56 | MLI, FAD |
| 4 | 1159 | 0.84 | 0.85 | 102 | HEM, RQX, EPH |
| 5 | 326 | 0.79 | 0.90 | 59 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2768 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 2733 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1922 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1904 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1833 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3VR8 · Mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum · 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 0.88
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 3VR8 · PDBe 3VR8 · UniProt Q33862 · UniProt O44074 · UniProt P92506 · UniProt P92507
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