MolNFT v1 · #142729 · protein
Anthrax toxin receptor 1-bound spent particles of seneca valley virus in acidic conditions
6ADL · VP1: “Anthrax toxin receptor 1-bound spent particles of seneca valley virus in acidic conditions”. Electron microscopy, 1 ligand (MG), 10 pockets (best druggability 0.71). MolNFT v1 #142729 on GenesisL1: 3D structure, binding sites…
- PDB
- 6ADL
- Type
- protein
- Length
- 891 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP3; VP2; Anthrax toxin receptor 1
- UniProt
- Q9H6X2
- Ligands
- MG
- Pockets
- 10 · best druggability 0.71
Structure
electron microscopy · 4 distinct chains · 15% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 230 | 5% helix, 35% strand | — |
| C | VP3 | protein | 230 | 7% helix, 23% strand | — |
| B | VP2 | protein | 246 | 10% helix, 29% strand | — |
| R | Anthrax toxin receptor 1 | protein | 185 | 43% helix, 21% strand | Q9H6X2 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.71 | 0.77 | 78 | empty |
| 2 | 200 | 0.55 | 0.79 | 26 | empty |
| 3 | 203 | 0.51 | 0.76 | 29 | empty |
| 4 | 149 | 0.43 | 0.75 | 28 | empty |
| 5 | 65 | 0.43 | 0.82 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2528 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2467 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 1701 Ų buried · 16 hydrogen bonds · protein-protein
- B–R · 841 Ų buried · 18 hydrogen bonds · protein-protein
- A–R · 377 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ADL · Anthrax Toxin Receptor 1-bound spent particles of Seneca Valley Virus in acidic conditions · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H6X2 · AlphaFold monomer V2.0 prediction for anthrax toxin receptor 1 (Q9H6X2) · a predicted model of the same protein · chain R against A, TM-score 0.90
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 Q9H6X2
- Elsewhere: RCSB PDB 6ADL · PDBe 6ADL · UniProt Q9H6X2
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