MolNFT v1 · #78399 · protein
Structure of the tvnirb form of thioalkalivibrio nitratireducens cytochrome C nitrite reductase with an oxidized GLN360 in a complex with hydroxylamine
3S7W · Eight-heme nitrite reductase: “Structure of the tvnirb form of thioalkalivibrio nitratireducens cytochrome C nitrite reductase with an…”. X-ray diffraction, 4 ligands (HEC, CA, NO2), 8 pockets (best druggability 0.88). MolNFT v1…
- PDB
- 3S7W
- Type
- protein
- Length
- 1,038 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, AZI
- Pockets
- 8 · best druggability 0.88
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 | 519 | 45% helix, 10% strand | Q5F2I3 |
Ligands and binding sites
- HEC · Heme C · ligand · 16 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NO2 · Nitrite ion · ion · 2 copies · chains A, B
- AZI · Azide ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.88 | 0.91 | 104 | HEC, NO2 |
| 2 | 536 | 0.87 | 0.93 | 87 | HEC, NO2 |
| 3 | 271 | 0.81 | 0.92 | 41 | HEC |
| 4 | 357 | 0.81 | 0.91 | 54 | HEC |
| 5 | 343 | 0.55 | 0.74 | 45 | AZI |
Interfaces
1 interface between chains.
- A–B · 1266 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 cofactor (heme c attachment).
Compared structures
- 3S7W · Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite… · 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 3S7W · PDBe 3S7W · UniProt Q5F2I3
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