MolNFT v1 · #8751 · protein
Cytochrome CD1 nitrite reductase, reduced form complexed to cn
1H9Y: “Cytochrome CD1 nitrite reductase, reduced form complexed to cn”. X-ray diffraction, 4 ligands (HEC, DHE, SO4), 8 pockets (best druggability 0.84). MolNFT v1 #8751 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1H9Y
- Type
- protein
- Length
- 1,039 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome CD1 nitrite reductase
- UniProt
- Q9FCQ0
- Ligands
- HEC, DHE, SO4, CYN
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome CD1 nitrite reductase | protein | 520 | 16% helix, 38% strand | Q9FCQ0 |
| B | Cytochrome CD1 nitrite reductase | protein | 519 | 17% helix, 39% strand | Q9FCQ0 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- DHE · Heme D · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CYN · Cyanide ion · ion · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.84 | 0.97 | 32 | empty |
| 2 | 518 | 0.75 | 0.83 | 61 | DHE, CYN, SO4 |
| 3 | 498 | 0.74 | 0.82 | 61 | DHE, CYN |
| 4 | 425 | 0.71 | 0.82 | 62 | HEC |
| 5 | 433 | 0.69 | 0.80 | 56 | HEC |
Interfaces
1 interface between chains.
- A–B · 1342 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 1H9Y · Cytochrome cd1 Nitrite Reductase, reduced form complexed to CN · 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 Q9FCQ0
- Elsewhere: RCSB PDB 1H9Y · PDBe 1H9Y · UniProt Q9FCQ0
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