MolNFT v1 · #77624 · protein
Structure of the thioalkalivibrio nitratireducens cytochrome C nitrite reductase in a complex with nitrite (full occupancy)
3RKH · Eight-heme nitrite reductase: “Structure of the thioalkalivibrio nitratireducens cytochrome C nitrite reductase in a complex with nitrite…”. X-ray diffraction, 3 ligands (HEC, CA, NO2), 5 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 3RKH
- Type
- protein
- Length
- 1,040 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eight-heme nitrite reductase
- UniProt
- Q5F2I3
- Ligands
- HEC, CA, NO2
- Pockets
- 5 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eight-heme nitrite reductase | protein | 520 | 45% helix, 10% strand | Q5F2I3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- NO2 · Nitrite ion · ion · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, 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 | 1140 | 0.89 | 0.91 | 147 | HEC, NO2 |
| 2 | 807 | 0.89 | 0.92 | 97 | HEC, NO2 |
| 3 | 355 | 0.82 | 0.92 | 48 | HEC |
| 4 | 220 | 0.54 | 0.77 | 26 | empty |
| 5 | 304 | 0.53 | 0.74 | 41 | 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
- 3RKH · Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a… · 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 3RKH · PDBe 3RKH · UniProt Q5F2I3
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