MolNFT v1 · #114899 · protein
Crystal structure of mitochondrial rhodoquinol-fumarate reductase from ascaris suum with ubiquinone-1
5C3J · Succinate dehydrogenase [ubiquinone] flavoprotein subunit…: “Crystal structure of mitochondrial rhodoquinol-fumarate reductase from ascaris suum with ubiquinone-1”. X-ray diffraction, 7 ligands (FAD, FES, SF4), 20 pockets (best…
- PDB
- 5C3J
- Type
- protein
- Length
- 2,296 residues
- Chains
- 8
- 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
- U1LRQ3, O44074, P92506, P92507
- Ligands
- FAD, FES, SF4, F3S, HEM, UQ1, EPH
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial (EC 1.3.5.1) | protein | 616 | 34% helix, 22% strand | U1LRQ3 |
| B, F | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (EC 1.3.5.1) | protein | 250 | 29% 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 | 69% helix, 2% strand | P92507 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, E, F
- 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
- UQ1 · Ubiquinone-1 · 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 | 1115 | 0.85 | 0.86 | 92 | HEM, UQ1, EPH |
| 2 | 292 | 0.85 | 0.96 | 56 | MLI, FAD |
| 3 | 267 | 0.85 | 0.97 | 57 | MLI, FAD |
| 4 | 1191 | 0.84 | 0.85 | 102 | HEM, UQ1, EPH |
| 5 | 1025 | 0.76 | 0.78 | 88 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2761 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2746 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 1947 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1947 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1846 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 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 0.90
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 5C3J · PDBe 5C3J · UniProt U1LRQ3 · UniProt O44074 · UniProt P92506 · UniProt P92507
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.