Research workbench
Crystal structure of apaf-1 card and caspase-9 card complex
Analyse Crystal structure of apaf-1 card and caspase-9 card complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RHW
- Type
- protein
- Length
- 564 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptotic protease-activating factor 1; Caspase-9
- EC
- 3.4.22.62
- UniProt
- O14727, P55211
- Ligands
- SO4, CL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Apoptotic protease-activating factor 1 | protein | 95 | 69% helix, 0% strand | O14727 |
| B, D | Apoptotic protease-activating factor 1 | protein | 92 | 77% helix, 0% strand | O14727 |
| E, F | Caspase-9 (EC 3.4.22.62) | protein | 95 | 67% helix, 0% strand | P55211 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, F, C, B, D, E
- CL · Chloride ion · ion · 2 copies · chains A, B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.81 | 0.83 | 99 | SO4, CL |
| 2 | 114 | 0.61 | 0.87 | 25 | SO4 |
| 3 | 80 | 0.38 | 0.77 | 21 | empty |
| 4 | 58 | 0.34 | 0.77 | 19 | empty |
Interfaces
12 interfaces between chains.
- A–E · 583 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 574 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 512 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 495 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 492 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4RHW · Crystal structure of Apaf-1 CARD and caspase-9 CARD complex · the same entry in another collection · chain F against F, TM-score 1.00
- P55211 · AlphaFold monomer V2.0 prediction for caspase-9 (P55211) · a predicted model of the same protein · chain E against A, TM-score 0.98
- O14727 · AlphaFold monomer V2.0 prediction for apoptotic protease-activating factor 1 (O14727) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 O14727
- Every structure of UniProt P55211
- Elsewhere: RCSB PDB 4RHW · PDBe 4RHW · UniProt O14727 · UniProt P55211
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