Research workbench
Crystal structure of caspase-8 in complex with aza-peptide michael acceptor inhibitor
Analyse Crystal structure of caspase-8 in complex with aza-peptide michael acceptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C2Z
- Type
- protein
- Length
- 242 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-8 P18 subunit; Caspase-8 P10 subunit; Aza-peptide inhibitor (5S, 8R…
- EC
- 3.4.22.-
- UniProt
- Q14790
- Ligands
- PHQ, MX5
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-8 P18 subunit (EC 3.4.22.-) | protein | 149 | 32% helix, 23% strand | Q14790 |
| B | Caspase-8 P10 subunit (EC 3.4.22.-) | protein | 90 | 36% helix, 20% strand | Q14790 |
| C | Aza-peptide inhibitor (5S, 8R, 11S)-8-(2-carboxyethyl) -14-[4-(3,4-dihydroquinolin-1(2H)-yl)-4-oxobutanoyl] -11-[(1R)-1-hydroxyethyl]-5-(2-methylpropyl)-3,6,9,12-tetraoxo -1-phenyl-2-oxa-4,7,10,13,14-pentaazahexadecan-16-oic acid | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · chains B, C
- MX5 · {1-[4-(3,4-dihydroquinolin-1(2H)-yl)-4-oxobutanoyl]hydrazino}acetic acid · ligand · chains A, B, C
- DTD · Dithiane diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.40 | 0.75 | 20 | DTD |
| 2 | 105 | 0.37 | 0.75 | 18 | MX5 |
Interfaces
3 interfaces between chains.
- A–B · 2236 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 282 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 2C2Z · Crystal structure of caspase-8 in complex with aza-peptide Michael acceptor inhibitor · the same entry in another collection · chain C against C, TM-score 1.00
- Q14790 · AlphaFold monomer V2.0 prediction for caspase-8 (Q14790) · a predicted model of the same protein · chain A against A, 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 2C2Z · PDBe 2C2Z · UniProt Q14790
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