Research workbench
Caspase-8 in complex with darpin-8.4
Analyse Caspase-8 in complex with darpin-8.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y1L
- Type
- protein
- Length
- 795 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-8; Darpin-8.4; Ac-ietd-cho
- EC
- 3.4.22.61
- UniProt
- Q14790
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-8 (EC 3.4.22.61) | protein | 150 | 31% helix, 28% strand | Q14790 |
| B | Caspase-8 (EC 3.4.22.61) | protein | 87 | 37% helix, 26% strand | Q14790 |
| C | Caspase-8 (EC 3.4.22.61) | protein | 148 | 32% helix, 27% strand | Q14790 |
| D | Caspase-8 (EC 3.4.22.61) | protein | 90 | 37% helix, 24% strand | Q14790 |
| E, F | Darpin-8.4 | protein | 156 | 53% helix, 0% strand | — |
| G, H | Ac-ietd-cho | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, H, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.73 | 0.82 | 43 | EDO |
| 2 | 93 | 0.37 | 0.75 | 23 | empty |
| 3 | 88 | 0.37 | 0.76 | 18 | empty |
| 4 | 88 | 0.35 | 0.75 | 22 | empty |
| 5 | 102 | 0.34 | 0.73 | 25 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2182 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2120 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1264 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1008 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 1006 Ų buried · 17 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 Q14790
- Elsewhere: RCSB PDB 2Y1L · PDBe 2Y1L · UniProt Q14790
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