MolNFT v1 · #67921 · protein
Homology model of avian polyomavirus asymmetric unit
3IYS · Major capsid protein VP1: “Homology model of avian polyomavirus asymmetric unit”. Electron microscopy, 11 pockets (best druggability 0.45). MolNFT v1 #67921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IYS
- Type
- protein
- Length
- 2,004 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- P13891
- Pockets
- 11 · best druggability 0.45
Structure
electron microscopy · 3 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Major capsid protein VP1 | protein | 337 | 0% helix, 0% strand | P13891 |
| D | Major capsid protein VP1 | protein | 321 | 0% helix, 0% strand | P13891 |
| F | Major capsid protein VP1 | protein | 335 | 0% helix, 0% strand | P13891 |
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.45 | 0.72 | 45 | empty |
| 2 | 145 | 0.42 | 0.73 | 36 | empty |
| 3 | 135 | 0.40 | 0.72 | 39 | empty |
| 4 | 102 | 0.38 | 0.73 | 22 | empty |
| 5 | 84 | 0.34 | 0.73 | 24 | empty |
Interfaces
7 interfaces between chains.
- B–F · 533 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 369 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 335 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 330 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 312 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IYS · Homology model of avian polyomavirus asymmetric unit · the same entry in another collection · chain D against D, 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 P13891
- Elsewhere: RCSB PDB 3IYS · PDBe 3IYS · UniProt P13891
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