MolNFT v1 · #19453 · protein
Cytochrome CD1 nitrite reductase, oxidised form
1QKS: “Cytochrome CD1 nitrite reductase, oxidised form”. X-ray diffraction, 3 ligands (HEC, DHE, SO4), 7 pockets (best druggability 0.86). MolNFT v1 #19453 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1QKS
- Type
- protein
- Length
- 1,118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome CD1 nitrite reductase
- UniProt
- P72181
- Ligands
- HEC, DHE, SO4
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome CD1 nitrite reductase | protein | 559 | 16% helix, 36% strand | P72181 |
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 · 6 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.86 | 0.90 | 87 | HEC, DHE, GOL |
| 2 | 694 | 0.84 | 0.88 | 83 | HEC, DHE, GOL |
| 3 | 219 | 0.83 | 0.97 | 34 | empty |
| 4 | 1079 | 0.77 | 0.79 | 86 | GOL |
| 5 | 58 | 0.29 | 0.75 | 19 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1383 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
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 P72181
- Elsewhere: RCSB PDB 1QKS · PDBe 1QKS · UniProt P72181
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