Research workbench
Crystal structure of an ATG7-ATG3 crosslinked complex
Analyse Crystal structure of an ATG7-ATG3 crosslinked complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GSL
- Type
- protein
- Length
- 1,556 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
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 598 | 34% helix, 24% strand | P38862 |
| B | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 592 | 35% helix, 25% strand | P38862 |
| C | Autophagy-related protein 3 | protein | 186 | 34% helix, 22% strand | P40344 |
| D | Autophagy-related protein 3 | protein | 180 | 33% helix, 24% strand | P40344 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.82 | 0.95 | 34 | empty |
| 2 | 234 | 0.82 | 0.94 | 35 | empty |
| 3 | 913 | 0.77 | 0.80 | 73 | empty |
| 4 | 955 | 0.74 | 0.77 | 82 | empty |
| 5 | 228 | 0.63 | 0.82 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2849 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 2215 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2139 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 226 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GSL · Crystal structure of an Atg7-Atg3 crosslinked complex · the same entry in another collection · chain D against D, TM-score 1.00
- P40344 · AlphaFold monomer V2.0 prediction for autophagy-related protein 3 (P40344) · a predicted model of the same protein · chain D against A, TM-score 0.92
- P38862 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme ATG7… · a predicted model of the same protein · chain B against A, TM-score 0.56
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 4GSL · PDBe 4GSL · UniProt P38862 · UniProt P40344
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