MolNFT v1 · #168885 · protein
Succinate-coenzyme Q reductase
6WU6 · Succinate dehydrogenase iron-sulfur subunit: “Succinate-coenzyme Q reductase”. Electron microscopy, 6 ligands (FES, SF4, F3S), 20 pockets (best druggability 0.88). MolNFT v1 #168885 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6WU6
- Type
- protein
- Length
- 2,781 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Succinate dehydrogenase iron-sulfur subunit; Succinate dehydrogenase; Succinate…
- EC
- 1.3.5.1
- UniProt
- A0A037Y3E8, C3TIP7, V0YWY6, B6I7Z5
- Ligands
- FES, SF4, F3S, HEM, FAD, NA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 44% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, F, J | Succinate dehydrogenase iron-sulfur subunit (EC 1.3.5.1) | protein | 238 | 29% helix, 6% strand | A0A037Y3E8 |
| C, G, K | Succinate dehydrogenase (EC 1.3.5.1) | protein | 114 | 83% helix, 0% strand | C3TIP7 |
| D, H, L | Succinate dehydrogenase hydrophobic membrane anchor subunit | protein | 105 | 84% helix, 0% strand | V0YWY6 |
| A, E, I | Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) | protein | 470 | 33% helix, 16% strand | B6I7Z5 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 3 copies · chains B, F, J
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains B, F, J
- F3S · FE3-S4 cluster · ligand · 3 copies · chains B, F, J
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains B, C, D, F, G, H, J, K, L
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, E, I
- NA · Sodium ion · metal · 3 copies · chains A, E, I
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 | 1086 | 0.88 | 0.89 | 97 | HEM |
| 2 | 1173 | 0.88 | 0.89 | 100 | HEM |
| 3 | 1140 | 0.87 | 0.88 | 95 | HEM |
| 4 | 366 | 0.81 | 0.90 | 70 | SF4 |
| 5 | 558 | 0.80 | 0.86 | 71 | FAD |
Interfaces
21 interfaces between chains.
- F–E · 2165 Ų buried · 31 hydrogen bonds · protein-protein
- B–A · 2161 Ų buried · 31 hydrogen bonds · protein-protein
- J–I · 2159 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1148 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 1144 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6WU6 · succinate-coenzyme Q reductase · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A037Y3E8
- Every structure of UniProt C3TIP7
- Every structure of UniProt V0YWY6
- Every structure of UniProt B6I7Z5
- Elsewhere: RCSB PDB 6WU6 · PDBe 6WU6 · UniProt A0A037Y3E8 · UniProt C3TIP7 · UniProt V0YWY6 · UniProt B6I7Z5
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