MolNFT v1 · #123300 · protein
Zebra fish caspase-3
5JFT · Caspase 3, apoptosis-related cysteine protease a: “Zebra fish caspase-3”. X-ray diffraction, 2 ligands (ACE, 0QE), 5 pockets (best druggability 0.72). MolNFT v1 #123300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JFT
- Type
- protein
- Length
- 481 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase 3, apoptosis-related cysteine protease a; ACE-asp-glu-val-ask
- UniProt
- Q98UI8
- Ligands
- ACE, 0QE
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase 3, apoptosis-related cysteine protease a | protein | 238 | 29% helix, 27% strand | Q98UI8 |
| B | Caspase 3, apoptosis-related cysteine protease a | protein | 235 | 29% helix, 26% strand | Q98UI8 |
| F, C | ACE-asp-glu-val-ask | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, F, B, C
- 0QE · Chloromethane · ion · 2 copies · chains A, F, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.72 | 0.81 | 39 | MRD |
| 2 | 99 | 0.53 | 0.84 | 24 | empty |
| 3 | 79 | 0.38 | 0.77 | 21 | empty |
| 4 | 50 | 0.32 | 0.77 | 20 | empty |
| 5 | 51 | 0.27 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2153 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 468 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 466 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5JFT · Zebra Fish Caspase-3 · the same entry in another collection · 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 Q98UI8
- Elsewhere: RCSB PDB 5JFT · PDBe 5JFT · UniProt Q98UI8
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