Research workbench
Structure of the DARC1 capsid
Analyse Structure 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
- 6TAP
- Type
- protein
- Length
- 686 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Activity-regulated cytoskeleton associated protein 1
- UniProt
- Q7K1U0
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.66
Structure
electron microscopy · 5 distinct chains · 54% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Activity-regulated cytoskeleton associated protein 1 | protein | 164 | 58% helix, 1% strand | Q7K1U0 |
| B | Activity-regulated cytoskeleton associated protein 1 | protein | 164 | 54% helix, 1% strand | Q7K1U0 |
| C | Activity-regulated cytoskeleton associated protein 1 | protein | 165 | 57% helix, 0% strand | Q7K1U0 |
| D | Activity-regulated cytoskeleton associated protein 1 | protein | 166 | 53% helix, 1% strand | Q7K1U0 |
| E | Activity-regulated cytoskeleton associated protein 1 | protein | 27 | 15% helix, 0% strand | Q7K1U0 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.66 | 0.74 | 78 | empty |
| 2 | 303 | 0.59 | 0.78 | 32 | empty |
| 3 | 245 | 0.51 | 0.75 | 32 | empty |
| 4 | 177 | 0.51 | 0.78 | 19 | empty |
| 5 | 109 | 0.50 | 0.81 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 889 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 795 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 686 Ų buried · 1 hydrogen bond · protein-protein
- C–E · 220 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 198 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 6TAP · PDBe 6TAP · UniProt Q7K1U0
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