MolNFT v1 · #98038 · protein
Plasticity of the quinone-binding site of the complex II homolog QUINOL:FUMARATE reductase
4KX6 · Fumarate reductase flavoprotein subunit: “Plasticity of the quinone-binding site of the complex II homolog QUINOL:FUMARATE reductase”. X-ray diffraction, 5 ligands (FAD, FES, F3S), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 4KX6
- Type
- protein
- Length
- 2,138 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit; Fumarate reductase (anaerobic), fe-S subunit…
- EC
- 1.3.99.1
- UniProt
- P00363, C5A1E7, C9QU46, P0A8Q3
- Ligands
- FAD, FES, F3S, SF4, MQ7
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Fumarate reductase flavoprotein subunit (EC 1.3.99.1) | protein | 577 | 38% helix, 20% strand | P00363 |
| B, N | Fumarate reductase (anaerobic), fe-S subunit | protein | 243 | 39% helix, 16% strand | C5A1E7 |
| C, O | Fumarate reductase subunit C | protein | 130 | 72% helix, 2% strand | C9QU46 |
| D, P | Fumarate reductase subunit D | protein | 119 | 76% helix, 1% strand | P0A8Q3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, M
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, N
- F3S · FE3-S4 cluster · ligand · 2 copies · chains B, N
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains B, N
- MQ7 · Menaquinone-7 · ligand · 2 copies · chains B, C, D, N, O, P
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 | 373 | 0.87 | 0.96 | 54 | FAD |
| 2 | 750 | 0.83 | 0.86 | 97 | FAD |
| 3 | 684 | 0.80 | 0.85 | 62 | empty |
| 4 | 261 | 0.79 | 0.91 | 28 | empty |
| 5 | 267 | 0.77 | 0.89 | 25 | empty |
Interfaces
13 interfaces between chains.
- M–N · 2744 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2703 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2381 Ų buried · 14 hydrogen bonds · protein-protein
- O–P · 2285 Ų buried · 14 hydrogen bonds · protein-protein
- N–O · 1503 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4KX6 · Plasticity of the qui -binding site of the complex II homolog quinol:fumarate reductase · the same entry in another collection · chain P against P, 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
- P0A8Q3 · AlphaFold monomer V2.0 prediction for fumarate reductase subunit D (P0A8Q3) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 C5A1E7
- Every structure of UniProt C9QU46
- Every structure of UniProt P0A8Q3
- Elsewhere: RCSB PDB 4KX6 · PDBe 4KX6 · UniProt P00363 · UniProt C5A1E7 · UniProt C9QU46 · UniProt P0A8Q3
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