Research workbench
The crystal structure of saccharomyces cerevisiae ATG8- ATG19(412-415) complex
Analyse The crystal structure of saccharomyces cerevisiae ATG8- ATG19(412-415) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZPN
- Type
- protein
- Length
- 453 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy-related protein 8; Saccharomyces cerevisiae ATG19(412-415)
- UniProt
- P38182
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autophagy-related protein 8 | protein | 111 | 30% helix, 23% strand | P38182 |
| B, D | Autophagy-related protein 8 | protein | 109 | 34% helix, 24% strand | P38182 |
| C | Autophagy-related protein 8 | protein | 108 | 34% helix, 24% strand | P38182 |
| E, F, G, H | Saccharomyces cerevisiae ATG19(412-415) | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.85 | 0.86 | 99 | SO4 |
| 2 | 411 | 0.68 | 0.80 | 68 | empty |
| 3 | 106 | 0.36 | 0.74 | 25 | empty |
| 4 | 82 | 0.34 | 0.74 | 14 | empty |
| 5 | 64 | 0.32 | 0.74 | 12 | empty |
Interfaces
16 interfaces between chains.
- A–C · 519 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 515 Ų buried · 6 hydrogen bonds · protein-protein
- C–G · 451 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 439 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 430 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2ZPN · The crystal structure of Saccharomyces cerevisiae Atg8- Atg19(412-415) complex · the same entry in another collection · chain H against H, TM-score 1.00
- P38182 · AlphaFold monomer V2.0 prediction for autophagy-related protein 8 (P38182) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P38182
- Elsewhere: RCSB PDB 2ZPN · PDBe 2ZPN · UniProt P38182
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