Research workbench
ATG8 transfer from ATG7 to ATG3: a distinctive E1-E2 architecture and mechanism in the autophagy pathway
Analyse ATG8 transfer from ATG7 to ATG3: a distinctive E1-E2 architecture and mechanism… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T7G
- Type
- protein
- Length
- 581 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 3
- UniProt
- P38862, P40344
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 286 | 27% helix, 35% strand | P38862 |
| B | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 273 | 26% helix, 36% strand | P38862 |
| D | Autophagy-related protein 3 | protein | 10 | 40% helix, 0% strand | P40344 |
| C | Autophagy-related protein 3 | protein | 12 | 67% helix, 0% strand | P40344 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.68 | 0.78 | 58 | empty |
| 2 | 212 | 0.59 | 0.81 | 38 | empty |
| 3 | 266 | 0.58 | 0.78 | 47 | empty |
| 4 | 161 | 0.51 | 0.79 | 24 | empty |
| 5 | 99 | 0.43 | 0.78 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1001 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 507 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 501 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 57 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3T7G · Atg8 transfer from Atg7 to Atg3: a distinctive E1-E2 architecture and mechanism in the… · the same entry in another collection · chain C against C, 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
- P40344 · AlphaFold monomer V2.0 prediction for autophagy-related protein 3 (P40344) · a predicted model of the same protein · chain C against A, TM-score 0.68
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 P40344
- Elsewhere: RCSB PDB 3T7G · PDBe 3T7G · UniProt P38862 · UniProt P40344
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