Research workbench
Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery
Analyse Structure of human ATG9A, the only transmembrane protein of the core autophagy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WQZ
- Type
- protein
- Length
- 1,715 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autophagy-related protein 9A
- UniProt
- Q7Z3C6
- Ligands
- LMN
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, A | Autophagy-related protein 9A | protein | 536 | 65% helix, 3% strand | Q7Z3C6 |
| F | Autophagy-related protein 9A | protein | 35 | 77% helix, 0% strand | Q7Z3C6 |
| E, D | Autophagy-related protein 9A | protein | 36 | 75% helix, 0% strand | Q7Z3C6 |
Ligands and binding sites
- LMN · Lauryl Maltose Neopentyl Glycol · ligand · 6 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.76 | 0.78 | 97 | LMN |
| 2 | 957 | 0.75 | 0.78 | 100 | LMN |
| 3 | 897 | 0.75 | 0.78 | 52 | empty |
| 4 | 929 | 0.75 | 0.78 | 57 | empty |
| 5 | 657 | 0.74 | 0.80 | 49 | empty |
Interfaces
12 interfaces between chains.
- B–A · 1662 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 1661 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 1661 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 610 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 610 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6WQZ · Structure of human ATG9A, the only transmembrane protein of the core autophagy machinery · the same entry in another collection · chain D against D, TM-score 1.00
- Q7Z3C6 · AlphaFold monomer V2.0 prediction for autophagy-related protein 9A (Q7Z3C6) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q7Z3C6
- Elsewhere: RCSB PDB 6WQZ · PDBe 6WQZ · UniProt Q7Z3C6
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