Research workbench
Structure of the two-fold capsomer of the DARC1 capsid
Analyse Structure of the two-fold capsomer of the DARC1 capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TAS
- Type
- protein
- Length
- 1,044 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activity-regulated cytoskeleton associated protein 1
- UniProt
- Q7K1U0
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.73
Structure
electron microscopy · 4 distinct chains · 52% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Activity-regulated cytoskeleton associated protein 1 | protein | 164 | 54% helix, 1% strand | Q7K1U0 |
| B, E | Activity-regulated cytoskeleton associated protein 1 | protein | 165 | 57% helix, 0% strand | Q7K1U0 |
| C, F | Activity-regulated cytoskeleton associated protein 1 | protein | 166 | 53% helix, 1% strand | Q7K1U0 |
| G, H | Activity-regulated cytoskeleton associated protein 1 | protein | 27 | 15% helix, 0% strand | Q7K1U0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.73 | 0.76 | 106 | empty |
| 2 | 1023 | 0.72 | 0.76 | 85 | empty |
| 3 | 711 | 0.69 | 0.77 | 72 | empty |
| 4 | 671 | 0.68 | 0.77 | 80 | empty |
| 5 | 582 | 0.66 | 0.76 | 75 | empty |
Interfaces
14 interfaces between chains.
- E–F · 901 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 847 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 811 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6TAS · Structure of the two-fold capsomer of the dArc1 capsid · the same entry in another collection · chain H against H, TM-score 1.00
- Q7K1U0 · AlphaFold monomer V2.0 prediction for activity-regulated cytoskeleton associated protein… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q7K1U0
- Elsewhere: RCSB PDB 6TAS · PDBe 6TAS · UniProt Q7K1U0
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