MolNFT v1 · #127831 · protein
Structure of the distal domain of mouse adenovirus 2 fibre, P21 native
5N8D · Fiber: “Structure of the distal domain of mouse adenovirus 2 fibre, P21 native”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.84). MolNFT v1 #127831 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5N8D
- Type
- protein
- Length
- 1,166 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber
- UniProt
- E7CH51
- Ligands
- CL
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Fiber | protein | 194 | 2% helix, 55% strand | E7CH51 |
| B, D | Fiber | protein | 195 | 4% helix, 57% strand | E7CH51 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.84 | 0.98 | 28 | empty |
| 2 | 192 | 0.83 | 0.97 | 29 | empty |
| 3 | 206 | 0.62 | 0.82 | 35 | empty |
| 4 | 179 | 0.61 | 0.83 | 30 | empty |
| 5 | 200 | 0.61 | 0.82 | 34 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1945 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1939 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1921 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1885 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1883 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5N8D · Structure of the distal domain of mouse adenovirus 2 fibre, P21 native · 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 E7CH51
- Elsewhere: RCSB PDB 5N8D · PDBe 5N8D · UniProt E7CH51
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.