Research workbench
Crystal structure of an ATG7-ATG10 crosslinked complex
Analyse Crystal structure of an ATG7-ATG10 crosslinked complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GSK
- Type
- protein
- Length
- 1,410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like modifier-activating enzyme ATG7; Ubiquitin-like-conjugating enzyme ATG10
- EC
- 6.3.2.-
- UniProt
- P38862, Q07879
- Ligands
- ZN
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 570 | 35% helix, 25% strand | P38862 |
| B | Ubiquitin-like modifier-activating enzyme ATG7 | protein | 572 | 37% helix, 26% strand | P38862 |
| Y | Ubiquitin-like-conjugating enzyme ATG10 (EC 6.3.2.-) | protein | 137 | 23% helix, 32% strand | Q07879 |
| Z | Ubiquitin-like-conjugating enzyme ATG10 (EC 6.3.2.-) | protein | 131 | 28% helix, 34% strand | Q07879 |
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
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.79 | 0.81 | 85 | empty |
| 2 | 1172 | 0.75 | 0.77 | 93 | empty |
| 3 | 173 | 0.68 | 0.87 | 29 | empty |
| 4 | 289 | 0.67 | 0.82 | 43 | empty |
| 5 | 198 | 0.67 | 0.85 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2717 Ų buried · 20 hydrogen bonds · protein-protein
- B–Y · 1827 Ų buried · 25 hydrogen bonds · protein-protein
- A–Z · 1815 Ų buried · 20 hydrogen bonds · protein-protein
- B–Z · 218 Ų buried · 1 hydrogen bond · protein-protein
- A–Y · 211 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4GSK · Crystal structure of an Atg7-Atg10 crosslinked complex · the same entry in another collection · chain Z against Z, TM-score 1.00
- Q07879 · AlphaFold monomer V2.0 prediction for ubiquitin-like-conjugating enzyme ATG10 (Q07879) · a predicted model of the same protein · chain Z against A, TM-score 0.96
- 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 0.55
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 Q07879
- Elsewhere: RCSB PDB 4GSK · PDBe 4GSK · UniProt P38862 · UniProt Q07879
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