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Cryo-EM structure of schizosaccharomyces pombe ATG9

Analyse Cryo-EM structure of schizosaccharomyces pombe ATG9 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7D0I
Type: protein
Length: 2,544 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Autophagy-related protein 9
UniProt: O74312
Ligands: LMN
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · 1 distinct chain · 69% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D, F, H, J, L	Autophagy-related protein 9	protein	424	69% helix, 4% strand	O74312

Ligands and binding sites

LMN · Lauryl Maltose Neopentyl Glycol · ligand · 12 copies · chains B, D, F, H, J, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1190	0.76	0.78	99	LMN
2	672	0.72	0.79	71	empty
3	415	0.66	0.79	48	empty
4	308	0.66	0.81	37	empty
5	510	0.66	0.77	50	empty

Interfaces

9 interfaces between chains.

B–F · 1489 Å² buried · 7 hydrogen bonds · protein-protein
H–L · 1485 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 1476 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 1467 Å² buried · 5 hydrogen bonds · protein-protein
H–J · 1461 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7D0I · Cryo-EM structure of Schizosaccharomyces pombe Atg9 · the same entry in another collection · chain L against L, TM-score 1.00
O74312 · AlphaFold monomer V2.0 prediction for autophagy-related protein 9 (O74312) · a predicted model of the same protein · chain J against A, TM-score 0.88

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 O74312
Elsewhere: RCSB PDB 7D0I · PDBe 7D0I · UniProt O74312

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