Research workbench
Anthrax toxin receptor 1-bound full particles of seneca valley virus in acidic conditions
Analyse Anthrax toxin receptor 1-bound full particles of seneca valley virus in acidic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ADM
- Type
- protein
- Length
- 973 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP3; VP2; VP4; Anthrax toxin receptor 1
- UniProt
- A0A1U9IRU2, Q9H6X2
- Ligands
- MG
- Pockets
- 14 · best druggability 0.68
Structure
electron microscopy · 5 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 258 | 8% helix, 30% strand | A0A1U9IRU2 |
| C | VP3 | protein | 228 | 6% helix, 32% strand | A0A1U9IRU2 |
| B | VP2 | protein | 267 | 11% helix, 33% strand | A0A1U9IRU2 |
| D | VP4 | protein | 35 | 11% helix, 11% strand | A0A1U9IRU2 |
| R | Anthrax toxin receptor 1 | protein | 185 | 37% helix, 23% strand | Q9H6X2 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.68 | 0.87 | 26 | empty |
| 2 | 516 | 0.67 | 0.78 | 52 | empty |
| 3 | 447 | 0.60 | 0.75 | 43 | empty |
| 4 | 201 | 0.55 | 0.79 | 34 | empty |
| 5 | 169 | 0.53 | 0.79 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–C · 3361 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 2751 Ų buried · 44 hydrogen bonds · protein-protein
- C–B · 1651 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 936 Ų buried · 9 hydrogen bonds · protein-protein
- B–R · 607 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ADM · Anthrax Toxin Receptor 1-bound full particles of Seneca Valley Virus in acidic conditions · the same entry in another collection · chain C against C, 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 A0A1U9IRU2
- Every structure of UniProt Q9H6X2
- Elsewhere: RCSB PDB 6ADM · PDBe 6ADM · UniProt A0A1U9IRU2 · UniProt Q9H6X2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.