MolNFT v1 · #126088 · protein
Sacbrood honeybee virus
5LSF · VP1: “Sacbrood honeybee virus”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.63). MolNFT v1 #126088 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LSF
- Type
- protein
- Length
- 781 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4
- UniProt
- Q9WCE9, Q6ITS8, I1U3P9, Q9IGK7
- Ligands
- CA
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 243 | 15% helix, 33% strand | Q9WCE9 |
| B | VP2 | protein | 239 | 11% helix, 42% strand | Q6ITS8 |
| C | VP3 | protein | 273 | 8% helix, 31% strand | I1U3P9 |
| D | VP4 | protein | 26 | 12% helix, 8% strand | Q9IGK7 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.63 | 0.89 | 22 | empty |
| 2 | 336 | 0.63 | 0.79 | 37 | empty |
| 3 | 60 | 0.55 | 0.88 | 17 | empty |
| 4 | 97 | 0.48 | 0.81 | 19 | empty |
| 5 | 116 | 0.39 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5523 Ų buried · 93 hydrogen bonds · protein-protein
- A–B · 1383 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1350 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 688 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5LSF · Sacbrood honeybee virus · 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 Q9WCE9
- Every structure of UniProt Q6ITS8
- Every structure of UniProt I1U3P9
- Every structure of UniProt Q9IGK7
- Elsewhere: RCSB PDB 5LSF · PDBe 5LSF · UniProt Q9WCE9 · UniProt Q6ITS8 · UniProt I1U3P9 · UniProt Q9IGK7
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