MolNFT v1 · #59395 · protein
Structure of free SV40 VP1 pentamer
3BWQ · Capsid protein VP1: “Structure of free SV40 VP1 pentamer”. X-ray diffraction, 14 pockets (best druggability 0.66). MolNFT v1 #59395 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3BWQ
- Type
- protein
- Length
- 1,319 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- P03087
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Capsid protein VP1 | protein | 267 | 8% helix, 40% strand | P03087 |
| B | Capsid protein VP1 | protein | 255 | 6% helix, 41% strand | P03087 |
| D | Capsid protein VP1 | protein | 265 | 6% helix, 41% strand | P03087 |
| E | Capsid protein VP1 | protein | 265 | 8% helix, 41% strand | P03087 |
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.66 | 0.93 | 24 | empty |
| 2 | 80 | 0.65 | 0.92 | 25 | empty |
| 3 | 67 | 0.64 | 0.93 | 23 | empty |
| 4 | 68 | 0.64 | 0.92 | 24 | empty |
| 5 | 80 | 0.64 | 0.91 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–E · 2322 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 2320 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2315 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2314 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 2304 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 3BWQ · Structure of free SV40 VP1 pentamer · 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 P03087
- Elsewhere: RCSB PDB 3BWQ · PDBe 3BWQ · UniProt P03087
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.