MolNFT v1 · #84517 · protein
VP16, a capsid protein of bacteriophage P23-77 (VP16-virus-derived)
3ZN5: “VP16, a capsid protein of bacteriophage P23-77 (VP16-virus-derived)”. X-ray diffraction, 1 ligand (CL), 18 pockets (best druggability 0.76). MolNFT v1 #84517 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZN5
- Type
- protein
- Length
- 1,325 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP16
- UniProt
- C8CHL4
- Ligands
- CL
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP16 | protein | 169 | 15% helix, 40% strand | C8CHL4 |
| B | VP16 | protein | 168 | 15% helix, 39% strand | C8CHL4 |
| C, F | VP16 | protein | 167 | 15% helix, 40% strand | C8CHL4 |
| D | VP16 | protein | 161 | 16% helix, 40% strand | C8CHL4 |
| E | VP16 | protein | 166 | 15% helix, 39% strand | C8CHL4 |
| G | VP16 | protein | 165 | 14% helix, 40% strand | C8CHL4 |
| H | VP16 | protein | 162 | 15% helix, 40% strand | C8CHL4 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.76 | 0.82 | 69 | empty |
| 2 | 879 | 0.73 | 0.77 | 70 | empty |
| 3 | 671 | 0.67 | 0.76 | 72 | empty |
| 4 | 217 | 0.60 | 0.81 | 29 | empty |
| 5 | 217 | 0.56 | 0.79 | 32 | empty |
Interfaces
14 interfaces between chains.
- E–F · 3234 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 3216 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 3173 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 3171 Ų buried · 51 hydrogen bonds · protein-protein
- D–F · 421 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ZN5 · VP16, a capsid protein of bacteriophage P23-77 (VP16-virus-derived) · 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 C8CHL4
- Elsewhere: RCSB PDB 3ZN5 · PDBe 3ZN5 · UniProt C8CHL4
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