Research workbench
Crystal structure of caspase-3 deve peptide complex
Analyse Crystal structure of caspase-3 deve peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IC4
- Type
- protein
- Length
- 938 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3 subunit P17; Caspase-3 subunit P12; Deve peptide
- EC
- 3.4.22.56
- UniProt
- P42574
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Caspase-3 subunit P17 (EC 3.4.22.56) | protein | 139 | 29% helix, 32% strand | P42574 |
| B, H | Caspase-3 subunit P12 (EC 3.4.22.56) | protein | 92 | 34% helix, 21% strand | P42574 |
| D, F | Caspase-3 subunit P12 (EC 3.4.22.56) | protein | 91 | 34% helix, 20% strand | P42574 |
| G | Caspase-3 subunit P17 (EC 3.4.22.56) | protein | 139 | 24% helix, 31% strand | P42574 |
| I, J, K, L | Deve peptide | protein | 4 | 0% helix, 50% strand | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.65 | 0.81 | 36 | empty |
| 2 | 280 | 0.63 | 0.80 | 38 | empty |
| 3 | 169 | 0.42 | 0.74 | 21 | empty |
Interfaces
21 interfaces between chains.
- C–D · 2151 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2143 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2112 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 2079 Ų buried · 31 hydrogen bonds · protein-protein
- F–H · 1431 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5IC4 · Crystal structure of caspase-3 DEVE peptide complex · the same entry in another collection · chain L against L, 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 P42574
- Elsewhere: RCSB PDB 5IC4 · PDBe 5IC4 · UniProt P42574
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