Research workbench
Crystal structure of saccharomyces cerevisiae ATG12-ATG5 conjugate bound to the N-terminal domain of ATG16
Analyse Crystal structure of saccharomyces cerevisiae ATG12-ATG5 conjugate bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W1S
- Type
- protein
- Length
- 362 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy protein 5; Autophagy protein 16; Ubiquitin-like protein ATG12
- UniProt
- Q12380, Q03818, P38316
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autophagy protein 5 | protein | 261 | 38% helix, 22% strand | Q12380 |
| B | Autophagy protein 16 | protein | 25 | 80% helix, 0% strand | Q03818 |
| C | Ubiquitin-like protein ATG12 | protein | 76 | 26% helix, 37% strand | P38316 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.59 | 0.81 | 35 | empty |
| 2 | 269 | 0.55 | 0.76 | 28 | empty |
| 3 | 83 | 0.36 | 0.76 | 18 | empty |
| 4 | 54 | 0.27 | 0.74 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1068 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 773 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3W1S · Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12380 · AlphaFold monomer V2.0 prediction for autophagy protein 5 (Q12380) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P38316 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ATG12 (P38316) · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q03818 · AlphaFold monomer V2.0 prediction for autophagy protein 16 (Q03818) · a predicted model of the same protein · chain B against A, TM-score 0.72
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 Q12380
- Every structure of UniProt Q03818
- Every structure of UniProt P38316
- Elsewhere: RCSB PDB 3W1S · PDBe 3W1S · UniProt Q12380 · UniProt Q03818 · UniProt P38316
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