Research workbench
Crystal structure of budding yeast ATG8 complexed with the helical aim of HFL1.
Analyse Crystal structure of budding yeast ATG8 complexed with the helical aim of HFL1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AAG
- Type
- protein
- Length
- 963 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transmembrane protein 184 homolog YKR051W,AUTOPHAGY-related protein 8
- UniProt
- P36142, A6ZKM4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Transmembrane protein 184 homolog YKR051W,AUTOPHAGY-related protein 8 | protein | 137 | 28% helix, 19% strand | P36142, A6ZKM4 |
| B | Transmembrane protein 184 homolog YKR051W,AUTOPHAGY-related protein 8 | protein | 138 | 28% helix, 20% strand | P36142, A6ZKM4 |
| C | Transmembrane protein 184 homolog YKR051W,AUTOPHAGY-related protein 8 | protein | 139 | 27% helix, 19% strand | P36142, A6ZKM4 |
| E | Transmembrane protein 184 homolog YKR051W,AUTOPHAGY-related protein 8 | protein | 136 | 28% helix, 21% strand | P36142, A6ZKM4 |
| F, G | Transmembrane protein 184 homolog YKR051W,AUTOPHAGY-related protein 8 | protein | 138 | 28% helix, 20% strand | P36142, A6ZKM4 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.75 | 0.79 | 91 | empty |
| 2 | 467 | 0.66 | 0.78 | 58 | empty |
| 3 | 411 | 0.65 | 0.78 | 38 | empty |
| 4 | 392 | 0.58 | 0.75 | 39 | empty |
| 5 | 219 | 0.56 | 0.78 | 23 | empty |
Interfaces
11 interfaces between chains.
- B–C · 1759 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1710 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 1703 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 1688 Ų buried · 31 hydrogen bonds · protein-protein
- E–G · 1652 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6AAG · Crystal structure of budding yeast Atg8 complexed with the helical AIM of Hfl1. · the same entry in another collection · chain B against B, TM-score 1.00
- A6ZKM4 · AlphaFold monomer V2.0 prediction for autophagy-related protein 8 (A6ZKM4) · a predicted model of the same protein · chain E against A, TM-score 0.80
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 P36142
- Every structure of UniProt A6ZKM4
- Elsewhere: RCSB PDB 6AAG · PDBe 6AAG · UniProt P36142 · UniProt A6ZKM4
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