MolNFT v1 · #60133 · protein
E. COLI quinol fumarate reductase frda T234A mutation
3CIR · Fumarate reductase flavoprotein subunit: “E. COLI quinol fumarate reductase frda T234A mutation”. X-ray diffraction, 4 ligands (FAD, FES, F3S), 20 pockets (best druggability 0.83). MolNFT v1 #60133 on GenesisL1: 3D structure…
- PDB
- 3CIR
- Type
- protein
- Length
- 2,029 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
- 1.3.99.1
- UniProt
- P00363, P0AC47, P0A8Q0, P0A8Q3
- Ligands
- FAD, FES, F3S, SF4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fumarate reductase flavoprotein subunit (EC 1.3.99.1) | protein | 541 | 38% helix, 18% strand | P00363 |
| B, N | Fumarate reductase iron-sulfur subunit (EC 1.3.99.1) | protein | 243 | 39% helix, 15% strand | P0AC47 |
| C, O | Fumarate reductase subunit C (EC 1.3.99.1) | protein | 130 | 74% helix, 2% strand | P0A8Q0 |
| D, P | Fumarate reductase subunit D (EC 1.3.99.1) | protein | 119 | 73% helix, 0% strand | P0A8Q3 |
| M | Fumarate reductase flavoprotein subunit (EC 1.3.99.1) | protein | 504 | 36% helix, 16% strand | P00363 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.83 | 0.89 | 77 | FAD |
| 2 | 720 | 0.82 | 0.86 | 92 | FAD |
| 3 | 314 | 0.79 | 0.89 | 29 | empty |
| 4 | 120 | 0.78 | 0.96 | 34 | empty |
| 5 | 262 | 0.78 | 0.90 | 29 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2717 Ų buried · 43 hydrogen bonds · protein-protein
- M–N · 2334 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2274 Ų buried · 10 hydrogen bonds · protein-protein
- O–P · 2271 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1432 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 covalent (flavinylation, covalent ligand).
Compared structures
- 3CIR · E. coli Quinol fumarate reductase FrdA T234A mutation · the same entry in another collection · chain P against P, TM-score 1.00
- P0AC47 · AlphaFold monomer V2.0 prediction for fumarate reductase iron-sulfur subunit (P0AC47) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P00363 · AlphaFold monomer V2.0 prediction for fumarate reductase flavoprotein subunit (P00363) · a predicted model of the same protein · chain M against A, TM-score 0.98
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 P0AC47
- Every structure of UniProt P0A8Q0
- Every structure of UniProt P0A8Q3
- Elsewhere: RCSB PDB 3CIR · PDBe 3CIR · UniProt P00363 · UniProt P0AC47 · UniProt P0A8Q0 · UniProt P0A8Q3
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