Research workbench
Semet regulator of nicotine degradation
Analyse Semet regulator of nicotine degradation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FHP
- Type
- protein
- Length
- 1,229 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicr
- UniProt
- A0A0B4KIF6
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicr | protein | 207 | 75% helix, 0% strand | A0A0B4KIF6 |
| B | Nicr | protein | 206 | 76% helix, 0% strand | A0A0B4KIF6 |
| C | Nicr | protein | 209 | 77% helix, 0% strand | A0A0B4KIF6 |
| D | Nicr | protein | 201 | 78% helix, 0% strand | A0A0B4KIF6 |
| E | Nicr | protein | 205 | 76% helix, 0% strand | A0A0B4KIF6 |
| F | Nicr | protein | 201 | 76% helix, 0% strand | A0A0B4KIF6 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, D, E, B, F
- MLA · Malonic acid · additive · 2 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.85 | 0.87 | 102 | empty |
| 2 | 1005 | 0.77 | 0.79 | 104 | MLA |
| 3 | 66 | 0.71 | 0.97 | 20 | GOL |
| 4 | 53 | 0.71 | 0.98 | 20 | empty |
| 5 | 51 | 0.70 | 0.98 | 18 | empty |
Interfaces
10 interfaces between chains.
- C–E · 2355 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 2349 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2341 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 570 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 409 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 modified (engineered).
Compared structures
- 5FHP · SeMet regulator of nicotine degradation · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0B4KIF6
- Elsewhere: RCSB PDB 5FHP · PDBe 5FHP · UniProt A0A0B4KIF6
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