Research workbench
E. COLI quinol fumarate reductase frda E49Q mutation
Analyse E. COLI quinol fumarate reductase frda E49Q mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B76
- Type
- protein
- Length
- 2,133 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fumarate reductase flavoprotein subunit; Fumarate reductase iron-sulfur protein; Fumarate…
- EC
- 1.3.99.1
- UniProt
- P00364, P0A8Q0, P0A8Q3
- Ligands
- FAD, FES, F3S, SF4, MQ7
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate reductase flavoprotein subunit | protein | 577 | 38% helix, 19% strand | — |
| B, N | Fumarate reductase iron-sulfur protein (EC 1.3.99.1) | protein | 243 | 37% helix, 14% strand | P00364 |
| C, O | Fumarate reductase subunit C | protein | 130 | 72% helix, 4% strand | P0A8Q0 |
| D, P | Fumarate reductase subunit D | protein | 119 | 70% helix, 0% strand | P0A8Q3 |
| M | Fumarate reductase flavoprotein subunit | protein | 572 | 30% helix, 10% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, 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 C, D, O, P
- FLC · Citrate anion · additive · 2 copies · chains A, M
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 | 0.86 | 0.94 | 57 | FLC, FAD |
| 2 | 794 | 0.85 | 0.88 | 107 | FLC, FAD |
| 3 | 669 | 0.80 | 0.84 | 51 | empty |
| 4 | 830 | 0.80 | 0.82 | 64 | empty |
| 5 | 230 | 0.79 | 0.91 | 23 | MQ7 |
Interfaces
13 interfaces between chains.
- M–N · 2714 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2676 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2362 Ų buried · 14 hydrogen bonds · protein-protein
- O–P · 2291 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1413 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 2B76 · E. coli Quinol fumarate reductase FrdA E49Q mutation · the same entry in another collection · chain P against P, TM-score 1.00
- 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 0.96
- P0A8Q0 · AlphaFold monomer V2.0 prediction for fumarate reductase subunit C (P0A8Q0) · a predicted model of the same protein · chain O against A, TM-score 0.93
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 P00364
- Every structure of UniProt P0A8Q0
- Every structure of UniProt P0A8Q3
- Elsewhere: RCSB PDB 2B76 · PDBe 2B76 · UniProt P00364 · UniProt P0A8Q0 · UniProt P0A8Q3
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