Research workbench
Crystal structure of Atg7CTD-Atg8 complex
Analyse Crystal structure of Atg7CTD-Atg8 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VH3
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Saccharomyces cerevisiae
- Molecule
- Ubiquitin-like modifier-activating enzyme ATG7; Autophagy-related protein 8
- UniProt
- P38862, P38182
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 320 | 42% helix, 16% strand | P38862 |
| B | Autophagy-related protein 8 | protein | 113 | 32% helix, 24% strand | P38182 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 349 | 0.67 | 0.81 | 52 | empty |
| 2 | 246 | 0.57 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1515 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3VH3 · Crystal structure of ATG7CTD-ATG8 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P38862 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme ATG7… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P38182 · AlphaFold monomer V2.0 prediction for autophagy-related protein 8 (P38182) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P38862
- Every structure of UniProt P38182
- Elsewhere: RCSB PDB 3VH3 · PDBe 3VH3 · UniProt P38862 · UniProt P38182
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