Research workbench
Structure of human polyomavirus 6 (HPYV6) VP1 pentamer
Analyse Structure of human polyomavirus 6 (HPYV6) VP1 pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PCG
- Type
- protein
- Length
- 1,329 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- D6QWI0
- Ligands
- NA, SCN
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 267 | 4% helix, 43% strand | D6QWI0 |
| B | VP1 | protein | 269 | 4% helix, 43% strand | D6QWI0 |
| C | VP1 | protein | 266 | 5% helix, 44% strand | D6QWI0 |
| D | VP1 | protein | 263 | 5% helix, 43% strand | D6QWI0 |
| E | VP1 | protein | 264 | 5% helix, 44% strand | D6QWI0 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D, E
- SCN · Thiocyanate ion · ion · 13 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.67 | 0.74 | 61 | empty |
| 2 | 284 | 0.52 | 0.75 | 32 | empty |
| 3 | 259 | 0.52 | 0.75 | 37 | empty |
| 4 | 260 | 0.51 | 0.75 | 32 | empty |
| 5 | 169 | 0.50 | 0.78 | 36 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2018 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 2015 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2012 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 2005 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1991 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4PCG · Structure of Human Polyomavirus 6 (HPyV6) 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 D6QWI0
- Elsewhere: RCSB PDB 4PCG · PDBe 4PCG · UniProt D6QWI0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.