Research workbench
Crystal structures of caspase-3 in complex with aza-peptide michael acceptor inhibitors.
Analyse Crystal structures of caspase-3 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
- 2C2M
- Type
- protein
- Length
- 252 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3 subunit P17; Caspase-3 subunit P12; Aza-peptide inhibitor (5S, 8R…
- EC
- 3.4.22.-
- UniProt
- P42574
- Ligands
- PHQ, MX4
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caspase-3 subunit P17 (EC 3.4.22.-) | protein | 146 | 25% helix, 29% strand | P42574 |
| B | Caspase-3 subunit P12 (EC 3.4.22.-) | protein | 103 | 30% helix, 16% strand | P42574 |
| C | Aza-peptide inhibitor (5S, 8R, 11S)-14-[4-(benzyloxy)-4- oxobutanoyl]-8-(2-carboxyethyl)-5-(carboxymethyl)-11-(1-methylethyl)- 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
- MX4 · {1-[4-(benzyloxy)-4-oxobutanoyl]hydrazino}acetic acid · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- A–B · 2273 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 2C2M · Crystal structures of caspase-3 in complex with aza-peptide Michael acceptor inhibitors. · the same entry in another collection · chain A against A, TM-score 1.00
- P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2C2M · PDBe 2C2M · UniProt P42574
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