Research workbench
Crystal structure of ATG7CTD-ATG8-mgatp complex
Analyse Crystal structure of ATG7CTD-ATG8-mgatp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VH4
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like modifier-activating enzyme ATG7; Autophagy-related protein 8
- UniProt
- P38862, P38182
- Ligands
- ATP, ZN, MG
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 320 | 43% helix, 16% strand | P38862 |
| B | Autophagy-related protein 8 | protein | 113 | 32% helix, 24% strand | P38182 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.74 | 0.81 | 83 | ATP, MG |
Interfaces
1 interface between chains.
- A–B · 1552 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3VH4 · Crystal structure of Atg7CTD-Atg8-MgATP 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 3VH4 · PDBe 3VH4 · UniProt P38862 · UniProt P38182
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.