MolNFT v1 · #16106 · protein
Crystal structure of the complex of nitrophorin 1 from rhodnius prolixus with histamine
1NP1: “Crystal structure of the complex of nitrophorin 1 from rhodnius prolixus with histamine”. X-ray diffraction, 3 ligands (HEM, HSM, PO4), 3 pockets (best druggability 0.75). MolNFT v1 #16106 on GenesisL1: 3D structure, binding sites…
- PDB
- 1NP1
- 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, HSM, PO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrophorin 1 | protein | 184 | 13% helix, 44% strand | Q26239 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- HSM · Histamine · ligand · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.75 | 0.84 | 43 | HEM, HSM |
| 2 | 412 | 0.73 | 0.83 | 44 | HEM, HSM |
| 3 | 53 | 0.31 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1NP1 · Crystal structure of the complex of nitrophorin 1 from rhodnius prolixus with histamine · 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 1NP1 · PDBe 1NP1 · UniProt Q26239
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