MolNFT v1 · #69179 · protein
Crystal structure of adeno-associated virus serotype 3B
3KIC · Capsid protein VP1: “Crystal structure of adeno-associated virus serotype 3B”. X-ray diffraction, 1 ligand (D5M), 20 pockets (best druggability 0.78). MolNFT v1 #69179 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KIC
- 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 0.78
Structure
x-ray diffraction · 1 distinct chain · 4% 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 | 4% 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 | 390 | 0.78 | 0.87 | 39 | empty |
| 2 | 400 | 0.78 | 0.87 | 40 | empty |
| 3 | 389 | 0.78 | 0.87 | 38 | empty |
| 4 | 384 | 0.77 | 0.87 | 38 | empty |
| 5 | 400 | 0.77 | 0.86 | 37 | empty |
Interfaces
45 interfaces between chains.
- C–D · 5305 Ų buried · 114 hydrogen bonds · protein-protein
- J–O · 5298 Ų buried · 111 hydrogen bonds · protein-protein
- I–Q · 5294 Ų buried · 110 hydrogen bonds · protein-protein
- A–D · 5287 Ų buried · 105 hydrogen bonds · protein-protein
- A–C · 5284 Ų buried · 107 hydrogen bonds · protein-protein
Compared structures
- 3KIC · Crystal structure of adeno-associated virus serotype 3B · the same entry in another collection · chain O against O, 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 3KIC · PDBe 3KIC · UniProt O56139
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.