MolNFT v1 · #6334 · protein
Caspase-8 specificity probed at subsite S4: crystal structure of the caspase-8-Z-devd-cho
1F9E · Caspase-8 alpha chain: “Caspase-8 specificity probed at subsite S4: crystal structure of the caspase-8-Z-devd-cho”. X-ray diffraction, 1 ligand (PHQ), 16 pockets (best druggability 0.76). MolNFT v1 #6334 on GenesisL1: 3D structure…
- PDB
- 1F9E
- Type
- protein
- Length
- 1,476 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-8 alpha chain; Caspase-8 beta chain; (PHQ)DEVD
- EC
- 3.4.22.-
- UniProt
- Q14790
- Ligands
- PHQ
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Caspase-8 alpha chain (EC 3.4.22.-) | protein | 153 | 31% helix, 25% strand | — |
| B, D, F, H, J, L | Caspase-8 beta chain | protein | 89 | 34% helix, 27% strand | Q14790 |
| Q, R, S, T, U, V | (PHQ)DEVD | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 6 copies · chains B, Q, D, R, F, S, H, T, J, U, L, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.76 | 0.81 | 59 | empty |
| 2 | 767 | 0.76 | 0.80 | 58 | empty |
| 3 | 718 | 0.74 | 0.80 | 55 | empty |
| 4 | 204 | 0.46 | 0.74 | 23 | empty |
| 5 | 139 | 0.44 | 0.76 | 21 | empty |
Interfaces
31 interfaces between chains.
- E–F · 2288 Ų buried · 33 hydrogen bonds · protein-protein
- K–L · 2269 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 2269 Ų buried · 32 hydrogen bonds · protein-protein
- I–J · 2265 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2259 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- 1F9E · Caspase-8 specificity probed at subsite S4: crystal structure of the caspase-8-Z-devd-cho · the same entry in another collection · chain U against U, TM-score 1.00
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 1F9E · PDBe 1F9E · UniProt Q14790
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