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Crystal structure of nitrophorin 4 triple mutant complex with ammonia
Analyse Crystal structure of nitrophorin 4 triple mutant complex with ammonia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GNW
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrophorin-4
- UniProt
- Q94734
- Ligands
- HEM, NH3, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 17% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitrophorin-4 | protein | 184 | 17% helix, 45% strand | Q94734 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NH3 · Ammonia · 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.77 | 0.99 | 27 | empty |
| 2 | 319 | 0.77 | 0.87 | 38 | HEM, NH3 |
| 3 | 325 | 0.76 | 0.87 | 37 | HEM, NH3 |
| 4 | 139 | 0.56 | 0.82 | 31 | empty |
| 5 | 74 | 0.31 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 Q94734
- Elsewhere: RCSB PDB 4GNW · PDBe 4GNW · UniProt Q94734
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