Research workbench
Crystal structure of S. cerevisiae ATG8 in complex with EDE1 (1220- 1247)
Analyse Crystal structure of S. cerevisiae ATG8 in complex with EDE1 (1220- 1247) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WY6
- Type
- protein
- Length
- 277 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy-related protein 8; Eh domain-containing and endocytosis protein 1
- UniProt
- A6ZKM4, P34216
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Autophagy-related protein 8 | protein | 114 | 32% helix, 23% strand | A6ZKM4 |
| A | Autophagy-related protein 8 | protein | 113 | 35% helix, 23% strand | A6ZKM4 |
| C | Eh domain-containing and endocytosis protein 1 | protein | 28 | 46% helix, 7% strand | P34216 |
| D | Eh domain-containing and endocytosis protein 1 | protein | 22 | 18% helix, 9% strand | P34216 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.49 | 0.79 | 18 | empty |
| 2 | 52 | 0.28 | 0.75 | 10 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1060 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 999 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 230 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 227 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 77 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 6WY6 · Crystal structure of S. cerevisiae Atg8 in complex with Ede1 (1220-1247) · the same entry in another collection · chain D against D, TM-score 1.00
- A6ZKM4 · AlphaFold monomer V2.0 prediction for autophagy-related protein 8 (A6ZKM4) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P34216 · AlphaFold monomer V2.0 prediction for eh domain-containing and endocytosis protein 1… · a predicted model of the same protein · chain C against A, TM-score 0.36
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 A6ZKM4
- Every structure of UniProt P34216
- Elsewhere: RCSB PDB 6WY6 · PDBe 6WY6 · UniProt A6ZKM4 · UniProt P34216
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