Research workbench
Crystal structure of the complex of caspase-3 with a bromomethoxyphenyl inhibitor
Analyse Crystal structure of the complex of caspase-3 with a bromomethoxyphenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RHQ
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-3
- EC
- 3.4.22.-
- UniProt
- P42574
- Ligands
- 0ZZ
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Caspase-3 (EC 3.4.22.-) | protein | 140 | 26% helix, 21% strand | P42574 |
| B, E | Caspase-3 (EC 3.4.22.-) | protein | 91 | 30% helix, 15% strand | P42574 |
Ligands and binding sites
- 0ZZ · 5-S-benzyl-3-({N-[(5-bromo-2-methoxyphenyl)acetyl]-L-valyl}amino)-2,3-dideoxy-5-thio-D-erythro-pentonic acid · ligand · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.65 | 0.79 | 37 | empty |
| 2 | 137 | 0.43 | 0.75 | 26 | 0ZZ |
| 3 | 111 | 0.38 | 0.75 | 20 | 0ZZ |
Interfaces
6 interfaces between chains.
- A–B · 2150 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 2147 Ų buried · 31 hydrogen bonds · protein-protein
- B–E · 1353 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 348 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 348 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1RHQ · Crystal structure of the complex of caspase-3 with a bromomethoxyphenyl inhibitor · the same entry in another collection · chain E against E, TM-score 1.00
- P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · a predicted model of the same protein · chain D 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 1RHQ · PDBe 1RHQ · UniProt P42574
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