Research workbench
Pentameric turret of bombyx mori cytoplasmic polyhedrosis virus after spike detaches.
Analyse Pentameric turret of bombyx mori cytoplasmic polyhedrosis virus after spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WHP
- Type
- protein
- Length
- 2,114 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP3
- UniProt
- Q914N6
- Ligands
- SAM, ATP
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Structural protein VP3 | protein | 1057 | 34% helix, 19% strand | Q914N6 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.76 | 0.78 | 96 | SAM |
| 2 | 894 | 0.75 | 0.79 | 99 | SAM |
| 3 | 466 | 0.68 | 0.79 | 53 | empty |
| 4 | 472 | 0.66 | 0.78 | 49 | SAM |
| 5 | 315 | 0.64 | 0.80 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 177 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7WHP · Pentameric turret of Bombyx mori cytoplasmic polyhedrosis virus after spike detaches. · 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 Q914N6
- Elsewhere: RCSB PDB 7WHP · PDBe 7WHP · UniProt Q914N6
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