Research workbench
Structure of the apoptotic protease-activating factor 1 bound to ADP
Analyse Structure of the apoptotic protease-activating factor 1 bound to ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z6T
- Type
- protein
- Length
- 2,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apoptotic protease activating factor 1
- UniProt
- O14727
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Apoptotic protease activating factor 1 | protein | 576 | 58% helix, 7% strand | O14727 |
| B, C | Apoptotic protease activating factor 1 | protein | 586 | 59% helix, 7% strand | O14727 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.84 | 0.85 | 98 | ADP |
| 2 | 887 | 0.84 | 0.85 | 87 | ADP |
| 3 | 736 | 0.83 | 0.86 | 77 | ADP |
| 4 | 745 | 0.83 | 0.86 | 74 | ADP |
| 5 | 1078 | 0.82 | 0.83 | 104 | empty |
Interfaces
5 interfaces between chains.
- A–B · 780 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 721 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 628 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 353 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 330 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Z6T · Structure of the apoptotic protease-activating factor 1 bound to ADP · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.84
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 1Z6T · PDBe 1Z6T · UniProt O14727
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