Research workbench
The Crystal Structure of Apaf from Biortus.
Analyse The Crystal Structure of Apaf from Biortus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8XQK
- Type
- protein
- Length
- 381 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Homo sapiens
- Molecule
- Apoptotic protease-activating factor 1
- UniProt
- O14727
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · resolution 2.85 · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Apoptotic protease-activating factor 1 | protein | 93 | 74% helix, 0% strand | O14727 |
| B | Apoptotic protease-activating factor 1 | protein | 98 | 67% helix, 0% strand | O14727 |
| C | Apoptotic protease-activating factor 1 | protein | 97 | 70% helix, 0% strand | O14727 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
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 | 244 | 0.52 | 0.76 | 27 | empty |
| 2 | 241 | 0.51 | 0.75 | 30 | empty |
| 3 | 77 | 0.37 | 0.77 | 19 | empty |
| 4 | 59 | 0.37 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 548 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 451 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 226 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- O14727 · AlphaFold monomer V2.0 prediction for apoptotic protease-activating factor 1 (O14727) · a predicted model of the same protein · chain A 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
- Elsewhere: RCSB PDB 8XQK · PDBe 8XQK · UniProt O14727
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.