Research workbench
Crystal structure of ATG7CTD-ATG8-mgatp complex in form II
Analyse Crystal structure of ATG7CTD-ATG8-mgatp complex in form II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YEC
- Type
- protein
- Length
- 811 residues
- Chains
- 4
- 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
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 304 | 46% helix, 17% strand | P38862 |
| B | Autophagy-related protein 8 | protein | 106 | 35% helix, 23% strand | P38182 |
| C | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 302 | 44% helix, 17% strand | P38862 |
| D | Autophagy-related protein 8 | protein | 99 | 38% helix, 18% strand | P38182 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.69 | 0.82 | 44 | ATP, MG |
| 2 | 275 | 0.58 | 0.78 | 49 | ATP, MG |
| 3 | 144 | 0.49 | 0.78 | 20 | empty |
| 4 | 124 | 0.46 | 0.77 | 19 | empty |
| 5 | 113 | 0.40 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2574 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 685 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 649 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YEC · Crystal structure of Atg7CTD-Atg8-MgATP complex in form II · the same entry in another collection · chain D against D, 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 0.98
- 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 0.98
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 P38862
- Every structure of UniProt P38182
- Elsewhere: RCSB PDB 5YEC · PDBe 5YEC · UniProt P38862 · UniProt P38182
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