Research workbench
Structure of cleaved, card domain deleted caspase-9
Analyse Structure of cleaved, card domain deleted caspase-9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JXQ
- Type
- protein
- Length
- 942 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caspase-9; Benzoxycarbonyl-val-ala-asp-fluoromethyl ketone inhibitor
- EC
- 3.4.22.-
- Ligands
- PHQ, CF0
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Caspase-9 (EC 3.4.22.-) | protein | 242 | 29% helix, 24% strand | — |
| B, D | Caspase-9 (EC 3.4.22.-) | protein | 226 | 28% helix, 24% strand | — |
| E, F | Benzoxycarbonyl-val-ala-asp-fluoromethyl ketone inhibitor | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- PHQ · benzyl chlorocarbonate · ligand · 2 copies · chains A, E, C, F
- CF0 · Fluoromethane · ion · 2 copies · chains A, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.86 | 0.87 | 154 | empty |
| 2 | 51 | 0.70 | 0.98 | 22 | empty |
| 3 | 128 | 0.61 | 0.86 | 24 | empty |
| 4 | 81 | 0.46 | 0.82 | 22 | empty |
| 5 | 62 | 0.40 | 0.81 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–B · 2032 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2017 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 903 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 338 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 337 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1JXQ · Structure of cleaved, CARD domain deleted Caspase-9 · 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
- Elsewhere: RCSB PDB 1JXQ · PDBe 1JXQ
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