Research workbench
Complex of potato ATG8 protein with a peptide from irish potato famine pathogen effector protein PEXRD54
Analyse Complex of potato ATG8 protein with a peptide from irish potato famine pathogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L83
- Type
- protein
- Length
- 234 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Asp-TRP-glu-ile-val; Autophagy-related protein
- UniProt
- M1C146
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Asp-TRP-glu-ile-val | protein | 5 | 0% helix, 40% strand | — |
| A, B | Autophagy-related protein | protein | 112 | 35% helix, 23% strand | M1C146 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.50 | 0.78 | 32 | empty |
| 2 | 126 | 0.47 | 0.78 | 21 | SO4 |
| 3 | 72 | 0.32 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 695 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 488 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 472 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5L83 · Complex of potato ATG8 protein with a peptide from Irish potato famine pathogen effector… · the same entry in another collection · chain C against C, TM-score 1.00
- M1C146 · AlphaFold monomer V2.0 prediction for autophagy-related protein 8C-like (M1C146) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 M1C146
- Elsewhere: RCSB PDB 5L83 · PDBe 5L83 · UniProt M1C146
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