MolNFT v1 · #23470 · protein
1.7 a crystal structure of H60C mutant of nitrophorin I. heme complexed with two molecules imidazole
1U17 · Nitrophorin 1: “1.7 a crystal structure of H60C mutant of nitrophorin I. heme complexed with two molecules imidazole”. X-ray diffraction, 2 ligands (HEM, PO4), 2 pockets (best druggability 0.77). MolNFT v1 #23470 on GenesisL1: 3D…
- PDB
- 1U17
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrophorin 1
- UniProt
- Q26239
- Ligands
- HEM, PO4
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrophorin 1 | protein | 185 | 12% helix, 44% strand | Q26239 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- IMD · Imidazole · additive · 4 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 | 559 | 0.77 | 0.84 | 44 | HEM, IMD |
| 2 | 540 | 0.76 | 0.83 | 43 | HEM, IMD |
Interfaces
1 interface between chains.
- A–B · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1U17 · 1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two… · 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 0.97
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 1U17 · PDBe 1U17 · UniProt Q26239
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