MolNFT v2 · #63916 · protein
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)
3FO3 · Eight-heme nitrite reductase: “Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite…”. X-ray diffraction at 1.4, 6 ligands (HEC, THJ, NA), 5 pockets (best druggability 0.89).…
- PDB
- 3FO3
- Type
- protein
- Length
- 1,038 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Thioalkalivibrio nitratireducens
- Molecule
- Eight-heme nitrite reductase
- UniProt
- Q5F2I3
- Ligands
- HEC, THJ, NA, CA, SO3, SO4
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · resolution 1.4 · 1 distinct chain · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eight-heme nitrite reductase | protein | 519 | 45% helix, 10% strand | Q5F2I3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- THJ · Thiosulfate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- SO3 · Sulfite ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 16 copies · chains A, B
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 8 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.89 | 0.91 | 146 | HEC, SO3, SO4 |
| 2 | 831 | 0.88 | 0.91 | 97 | HEC, SO3, CA |
| 3 | 387 | 0.83 | 0.91 | 49 | HEC |
| 4 | 243 | 0.56 | 0.77 | 27 | PG6 |
| 5 | 240 | 0.50 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1277 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 3FO3 · Structure of the thioalkalivibrio nitratireducens cytochrome C nitrite reductase reduced… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5F2I3
- Elsewhere: RCSB PDB 3FO3 · PDBe 3FO3 · UniProt Q5F2I3
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