MolNFT v1 · #64990 · protein
Caspase-3 binds diverse P4 residues in peptides
3GJQ · Caspase-3 subunit P17: “Caspase-3 binds diverse P4 residues in peptides”. X-ray diffraction, 1 ligand (ACE), 2 pockets (best druggability 0.65). MolNFT v1 #64990 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GJQ
- Type
- protein
- Length
- 474 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3 subunit P17; Caspase-3 subunit P12; Peptide inhibitor
- EC
- 3.4.22.56
- UniProt
- P42574
- Ligands
- ACE
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-3 subunit P17 (EC 3.4.22.56) | protein | 141 | 26% helix, 30% strand | P42574 |
| B | Caspase-3 subunit P12 (EC 3.4.22.56) | protein | 92 | 34% helix, 21% strand | P42574 |
| C | Caspase-3 subunit P17 (EC 3.4.22.56) | protein | 140 | 29% helix, 31% strand | P42574 |
| D | Caspase-3 subunit P12 (EC 3.4.22.56) | protein | 93 | 33% helix, 20% strand | P42574 |
| E, F | Peptide inhibitor | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.65 | 0.80 | 31 | empty |
| 2 | 52 | 0.27 | 0.74 | 13 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2227 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2168 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1430 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 463 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 458 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 P42574
- Elsewhere: RCSB PDB 3GJQ · PDBe 3GJQ · UniProt P42574
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