Research workbench
Structure to function correlations for adeno-associated virus serotype 1
Analyse Structure to function correlations for adeno-associated virus serotype 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NG9
- Type
- protein
- Length
- 5,200 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein
- UniProt
- Q9WBP8
- Ligands
- ADE, CYT
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Capsid protein | protein | 520 | 7% helix, 36% strand | Q9WBP8 |
Ligands and binding sites
- ADE · Adenine · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- CYT · 6-aminopyrimidin-2(1H)-one · ligand · 10 copies · chains A, H, B, G, E, C, I, D, F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.76 | 0.86 | 38 | empty |
| 2 | 359 | 0.75 | 0.86 | 33 | empty |
| 3 | 362 | 0.75 | 0.86 | 34 | empty |
| 4 | 366 | 0.74 | 0.85 | 36 | empty |
| 5 | 55 | 0.72 | 0.99 | 22 | empty |
Interfaces
21 interfaces between chains.
- E–G · 5239 Ų buried · 107 hydrogen bonds · protein-protein
- A–D · 5227 Ų buried · 107 hydrogen bonds · protein-protein
- C–F · 5217 Ų buried · 104 hydrogen bonds · protein-protein
- B–G · 5215 Ų buried · 107 hydrogen bonds · protein-protein
- B–E · 5213 Ų buried · 108 hydrogen bonds · protein-protein
Compared structures
- 3NG9 · Structure to Function Correlations for Adeno-associated Virus Serotype 1 · 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 Q9WBP8
- Elsewhere: RCSB PDB 3NG9 · PDBe 3NG9 · UniProt Q9WBP8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.