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Cryo-EM structure of complete transmembrane channel E289A mutant vibrio cholerae cytolysin

Analyse Cryo-EM structure of complete transmembrane channel E289A mutant vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7YL9
Type: protein
Length: 4,067 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemolysin
UniProt: A0A0H6SZL4
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 4% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, I, J, K, L, M, N	Hemolysin	protein	581	4% helix, 50% strand	A0A0H6SZL4

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	189	0.82	0.96	48	empty
2	180	0.79	0.93	31	empty
3	1190	0.76	0.78	127	empty
4	79	0.75	0.97	19	empty
5	376	0.75	0.85	59	empty

Interfaces

13 interfaces between chains.

H–I · 2763 Å² buried · 74 hydrogen bonds · protein-protein
M–N · 2715 Å² buried · 71 hydrogen bonds · protein-protein
H–N · 2715 Å² buried · 59 hydrogen bonds · protein-protein
J–K · 2711 Å² buried · 64 hydrogen bonds · protein-protein
K–L · 2685 Å² buried · 72 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide (disulfide).

Compared structures

7YL9 · Cryo-EM structure of complete transmembrane channel E289A mutant Vibrio cholerae Cytolysin · 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 A0A0H6SZL4
Elsewhere: RCSB PDB 7YL9 · PDBe 7YL9 · UniProt A0A0H6SZL4

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