MolNFT v1 · #143330 · protein
Escherichia COLI QUINOL:FUMARATE reductase crystallized without dicarboxylate
6AWF · Fumarate reductase flavoprotein subunit: “Escherichia COLI QUINOL:FUMARATE reductase crystallized without dicarboxylate”. X-ray diffraction, 5 ligands (FAD, FES, F3S), 20 pockets (best druggability 0.86). MolNFT v1 #143330 on…
- PDB
- 6AWF
- Type
- protein
- Length
- 2,036 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit; Fumarate reductase iron-sulfur subunit; Fumarate…
- EC
- 1.3.5.4, 1.3.5.1
- UniProt
- P00363, P0AC49, B7MKV9, B7MKV8
- Ligands
- FAD, FES, F3S, SF4, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate reductase flavoprotein subunit (EC 1.3.5.4) | protein | 573 | 38% helix, 20% strand | P00363 |
| B | Fumarate reductase iron-sulfur subunit (EC 1.3.5.1) | protein | 241 | 40% helix, 17% strand | P0AC49 |
| C, G | Fumarate reductase subunit C | protein | 130 | 72% helix, 2% strand | B7MKV9 |
| D | Fumarate reductase subunit D | protein | 119 | 73% helix, 1% strand | B7MKV8 |
| E | Fumarate reductase flavoprotein subunit (EC 1.3.5.4) | protein | 487 | 38% helix, 19% strand | P00363 |
| F | Fumarate reductase iron-sulfur subunit (EC 1.3.5.1) | protein | 238 | 39% helix, 14% strand | P0AC49 |
| H | Fumarate reductase subunit D | protein | 118 | 75% helix, 1% strand | B7MKV8 |
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
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, F
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, F
- PO4 · Phosphate ion · ion · 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 | 699 | 0.86 | 0.90 | 96 | FAD, PO4 |
| 2 | 372 | 0.85 | 0.93 | 60 | FAD, PO4 |
| 3 | 257 | 0.78 | 0.90 | 27 | empty |
| 4 | 239 | 0.76 | 0.89 | 25 | empty |
| 5 | 63 | 0.73 | 0.98 | 20 | SF4 |
Interfaces
14 interfaces between chains.
- A–B · 2648 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2502 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2326 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 2324 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1465 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 6AWF · Escherichia coli quinol:fumarate reductase crystallized without dicarboxylate · the same entry in another collection · chain H against H, TM-score 1.00
- P00363 · AlphaFold monomer V2.0 prediction for fumarate reductase flavoprotein subunit (P00363) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0AC49 · AlphaFold monomer V2.0 prediction for fumarate reductase iron-sulfur subunit (P0AC49) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P00363
- Every structure of UniProt P0AC49
- Every structure of UniProt B7MKV9
- Every structure of UniProt B7MKV8
- Elsewhere: RCSB PDB 6AWF · PDBe 6AWF · UniProt P00363 · UniProt P0AC49 · UniProt B7MKV9 · UniProt B7MKV8
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