Research workbench
Crystal structure of adeno-associated virus serotype 3B
Analyse Crystal structure of adeno-associated virus serotype 3B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KIE
- Type
- protein
- Length
- 10,400 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- O56139
- Ligands
- D5M
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | Capsid protein VP1 | protein | 520 | 5% helix, 35% strand | O56139 |
Ligands and binding sites
- D5M · 2'-deoxyadenosine-5'-monophosphate · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
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 | 383 | 0.79 | 0.88 | 38 | empty |
| 2 | 365 | 0.78 | 0.88 | 40 | empty |
| 3 | 373 | 0.78 | 0.88 | 38 | empty |
| 4 | 375 | 0.78 | 0.87 | 38 | empty |
| 5 | 384 | 0.78 | 0.87 | 37 | empty |
Interfaces
45 interfaces between chains.
- C–D · 5315 Ų buried · 107 hydrogen bonds · protein-protein
- J–O · 5307 Ų buried · 106 hydrogen bonds · protein-protein
- B–H · 5299 Ų buried · 104 hydrogen bonds · protein-protein
- A–D · 5298 Ų buried · 104 hydrogen bonds · protein-protein
- F–P · 5295 Ų buried · 107 hydrogen bonds · protein-protein
Compared structures
- 3KIE · Crystal structure of adeno-associated virus serotype 3B · 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 O56139
- Elsewhere: RCSB PDB 3KIE · PDBe 3KIE · UniProt O56139
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