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Cryo-EM structure of aerolysin prepore

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

PDB: 5JZH
Type: protein
Length: 5,936 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aerolysin
UniProt: P09167
Pockets: 20 · best druggability 0.73

Structure

electron microscopy · 1 distinct chain · 18% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N	Aerolysin	protein	424	18% helix, 31% strand	P09167

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	916	0.73	0.77	116	empty
2	882	0.69	0.75	80	empty
3	642	0.69	0.77	69	empty
4	562	0.69	0.78	62	empty
5	140	0.68	0.89	25	empty

Interfaces

21 interfaces between chains.

H–N · 2028 Å² buried · 39 hydrogen bonds · protein-protein
I–J · 2027 Å² buried · 39 hydrogen bonds · protein-protein
E–F · 2025 Å² buried · 39 hydrogen bonds · protein-protein
J–K · 2024 Å² buried · 39 hydrogen bonds · protein-protein
M–N · 2024 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

5JZH · Cryo-EM structure of aerolysin prepore · the same entry in another collection · chain H against H, TM-score 1.00

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 P09167
Elsewhere: RCSB PDB 5JZH · PDBe 5JZH · UniProt P09167

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