MolNFT v1 · #119806 · protein

Cryo-EM structure of the lysenin pore

5GAQ: “Cryo-EM structure of the lysenin pore”. Electron microscopy, 20 pockets (best druggability 0.77). MolNFT v1 #119806 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GAQ
Type: protein
Length: 2,592 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysenin
UniProt: O18423
Pockets: 20 · best druggability 0.77

Structure

electron microscopy · 1 distinct chain · 1% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I	Lysenin	protein	288	1% helix, 62% strand	O18423

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	359	0.77	0.87	65	empty
2	388	0.74	0.85	57	empty
3	358	0.74	0.85	50	empty
4	371	0.73	0.85	51	empty
5	357	0.72	0.84	53	empty

Interfaces

18 interfaces between chains.

B–C · 3537 Å² buried · 80 hydrogen bonds · protein-protein
D–E · 3536 Å² buried · 80 hydrogen bonds · protein-protein
A–I · 3536 Å² buried · 80 hydrogen bonds · protein-protein
F–G · 3535 Å² buried · 80 hydrogen bonds · protein-protein
H–I · 3532 Å² buried · 80 hydrogen bonds · protein-protein

Compared structures

5GAQ · Cryo-EM structure of the Lysenin Pore · the same entry in another collection · chain I against I, TM-score 1.00
O18423 · AlphaFold monomer V2.0 prediction for lysenin (O18423) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 O18423
Elsewhere: RCSB PDB 5GAQ · PDBe 5GAQ · UniProt O18423

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.