Research workbench
E. COLI quinol fumarate reductase frda E245Q mutation
Analyse E. COLI quinol fumarate reductase frda E245Q mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VPN
- Type
- protein
- Length
- 2,146 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, P0A8Q0, P0A8Q3
- Ligands
- FAD, FES, F3S, SF4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate reductase flavoprotein subunit (EC 1.3.5.4) | protein | 577 | 37% helix, 19% strand | P00363 |
| B, F | Fumarate reductase iron-sulfur subunit (EC 1.3.5.1) | protein | 243 | 40% helix, 17% strand | P0AC49 |
| C, G | Fumarate reductase subunit C | protein | 130 | 74% helix, 2% strand | P0A8Q0 |
| D, H | Fumarate reductase subunit D | protein | 119 | 73% helix, 1% strand | P0A8Q3 |
| E | Fumarate reductase flavoprotein subunit (EC 1.3.5.4) | protein | 585 | 37% helix, 19% strand | P00363 |
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
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 | 394 | 0.87 | 0.95 | 56 | FAD |
| 2 | 349 | 0.85 | 0.95 | 55 | FAD |
| 3 | 696 | 0.80 | 0.84 | 62 | empty |
| 4 | 326 | 0.80 | 0.90 | 32 | empty |
| 5 | 285 | 0.79 | 0.90 | 26 | empty |
Interfaces
13 interfaces between chains.
- E–F · 2725 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2679 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2397 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 2394 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1397 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5VPN · E. coli Quinol fumarate reductase FrdA E245Q mutation · 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 E 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 B 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 P0A8Q0
- Every structure of UniProt P0A8Q3
- Elsewhere: RCSB PDB 5VPN · PDBe 5VPN · UniProt P00363 · UniProt P0AC49 · UniProt P0A8Q0 · UniProt P0A8Q3
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