MolNFT v1 · #72998 · protein
Crystal structure of the complex of nitrophorin 1 from rhodnius prolixus with cyanide
3NP1: “Crystal structure of the complex of nitrophorin 1 from rhodnius prolixus with cyanide”. X-ray diffraction, 3 ligands (HEM, CYN, PO4), 2 pockets (best druggability 0.74). MolNFT v1 #72998 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3NP1
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrophorin 1
- UniProt
- Q26239
- Ligands
- HEM, CYN, PO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrophorin 1 | protein | 184 | 15% helix, 46% strand | Q26239 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.74 | 0.84 | 43 | CYN, HEM |
| 2 | 415 | 0.72 | 0.82 | 41 | CYN, HEM |
Interfaces
1 interface between chains.
- A–B · 61 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3NP1 · Crystal structure of the complex of nitrophorin 1 from rhodnius prolixus with cyanide · the same entry in another collection · chain A against A, TM-score 1.00
- Q26239 · AlphaFold monomer V2.0 prediction for nitrophorin-1 (Q26239) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q26239
- Elsewhere: RCSB PDB 3NP1 · PDBe 3NP1 · UniProt Q26239
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