MolNFT v1 · #15446 · protein
Following the C heme reduction in nitrite reductase from pseudomonas aeruginosa
1N50: “Following the C heme reduction in nitrite reductase from pseudomonas aeruginosa”. X-ray diffraction, 2 ligands (HEC, DHE), 6 pockets (best druggability 0.85). MolNFT v1 #15446 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1N50
- Type
- protein
- Length
- 1,077 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrite reductase
- EC
- 1.9.3.2
- UniProt
- P24474
- Ligands
- HEC, DHE
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrite reductase (EC 1.9.3.2) | protein | 538 | 16% helix, 38% strand | P24474 |
| B | Nitrite reductase (EC 1.9.3.2) | protein | 539 | 15% helix, 37% strand | P24474 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.85 | 0.87 | 106 | HEC, DHE |
| 2 | 966 | 0.85 | 0.86 | 107 | HEC, DHE |
| 3 | 478 | 0.84 | 0.90 | 52 | empty |
| 4 | 1104 | 0.76 | 0.78 | 76 | empty |
| 5 | 93 | 0.35 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3274 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 1N50 · Following the C heme reduction in nitrite reductase from pseudomonas aeruginosa · the same entry in another collection · chain A against A, TM-score 1.00
- P24474 · AlphaFold monomer V2.0 prediction for nitrite reductase (P24474) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P24474
- Elsewhere: RCSB PDB 1N50 · PDBe 1N50 · UniProt P24474
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