Research workbench
Anthrax Toxin Receptor 1-bound the Seneca Valley Virus in neutral conditions
Analyse Anthrax Toxin Receptor 1-bound the Seneca Valley Virus in neutral conditions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ADR
- Type
- protein
- Length
- 976 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.38
- Source
- Homo sapiens; Seneca valley virus
- Molecule
- VP1; VP3; vp2; VP4; Anthrax toxin receptor 1
- UniProt
- Q9H6X2
- Ligands
- MG
- Pockets
- 13 · best druggability 0.72
Structure
electron microscopy · resolution 3.38 · 5 distinct chains · 13% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 258 | 6% helix, 33% strand | — |
| C | VP3 | protein | 231 | 7% helix, 31% strand | — |
| B | vp2 | protein | 267 | 7% helix, 30% strand | — |
| D | VP4 | protein | 35 | 11% helix, 11% strand | — |
| R | Anthrax toxin receptor 1 | protein | 185 | 40% helix, 22% 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.72 | 0.76 | 87 | empty |
| 2 | 164 | 0.67 | 0.87 | 23 | empty |
| 3 | 193 | 0.55 | 0.79 | 24 | empty |
| 4 | 231 | 0.51 | 0.76 | 28 | empty |
| 5 | 153 | 0.47 | 0.77 | 29 | empty |
Interfaces
8 interfaces between chains.
- A–C · 3410 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2740 Ų buried · 44 hydrogen bonds · protein-protein
- C–B · 1715 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 951 Ų buried · 10 hydrogen bonds · protein-protein
- B–R · 689 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ADR · Anthrax toxin receptor 1-bound the seneca valley virus in neutral 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 0.91
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 6ADR · PDBe 6ADR · UniProt Q9H6X2
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