Research workbench
Crystal structure of the human adenovirus type 14 fiber knob
Analyse Crystal structure of the human adenovirus type 14 fiber knob in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F0Y
- Type
- protein
- Length
- 1,783 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- Q8V791
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, I | Fiber protein | protein | 198 | 12% helix, 41% strand | Q8V791 |
| G | Fiber protein | protein | 199 | 12% helix, 41% strand | Q8V791 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, C, H
- IMD · Imidazole · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.79 | 0.86 | 39 | empty |
| 2 | 470 | 0.79 | 0.86 | 39 | empty |
| 3 | 485 | 0.77 | 0.85 | 39 | empty |
| 4 | 599 | 0.66 | 0.76 | 62 | empty |
| 5 | 458 | 0.63 | 0.77 | 56 | empty |
Interfaces
12 interfaces between chains.
- G–H · 1118 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1109 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1106 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1099 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1090 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3F0Y · Crystal structure of the human Adenovirus type 14 fiber knob · 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 Q8V791
- Elsewhere: RCSB PDB 3F0Y · PDBe 3F0Y · UniProt Q8V791
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