MolNFT v1 · #103817 · protein
Caspase-8 specific unnatural amino acid peptides
4PS1: “Caspase-8 specific unnatural amino acid peptides”. X-ray diffraction, 11 pockets (best druggability 0.68). MolNFT v1 #103817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PS1
- Type
- protein
- Length
- 969 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-8; (BAL)LQ(HYP)(1U8) peptide
- EC
- 3.4.22.61
- UniProt
- Q14790
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-8 (EC 3.4.22.61) | protein | 238 | 33% helix, 23% strand | Q14790 |
| B | Caspase-8 (EC 3.4.22.61) | protein | 238 | 33% helix, 23% strand | Q14790 |
| C | Caspase-8 (EC 3.4.22.61) | protein | 237 | 33% helix, 23% strand | Q14790 |
| D | Caspase-8 (EC 3.4.22.61) | protein | 236 | 33% helix, 23% strand | Q14790 |
| E, F, G, H | (BAL)LQ(HYP)(1U8) peptide | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.68 | 0.77 | 45 | empty |
| 2 | 546 | 0.66 | 0.77 | 38 | empty |
| 3 | 403 | 0.64 | 0.78 | 47 | empty |
| 4 | 123 | 0.42 | 0.76 | 19 | empty |
| 5 | 104 | 0.42 | 0.77 | 21 | DTT |
Interfaces
7 interfaces between chains.
- B–F · 504 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 504 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 500 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 498 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (nonstandard, hydroxylation).
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 4PS1 · PDBe 4PS1 · UniProt Q14790
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