MolNFT v1 · #126287 · protein

Cryoem structure of the membrane pore complex of pneumolysin at 4.5A

5LY6: “Cryoem structure of the membrane pore complex of pneumolysin at 4.5A”. Electron microscopy, 6 pockets (best druggability 0.68). MolNFT v1 #126287 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LY6
Type: protein
Length: 471 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pneumolysin
UniProt: Q04IN8
Pockets: 6 · best druggability 0.68

Structure

electron microscopy · 1 distinct chain · 13% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Pneumolysin	protein	471	13% helix, 36% strand	Q04IN8

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.68	0.92	21	empty
2	156	0.61	0.84	30	empty
3	170	0.55	0.80	31	empty
4	60	0.44	0.82	19	empty
5	83	0.42	0.80	17	empty

Compared structures

5LY6 · CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A · the same entry in another collection · chain B against B, TM-score 1.00
Q04IN8 · AlphaFold monomer V2.0 prediction for pneumolysin (Q04IN8) · a predicted model of the same protein · chain B against A, TM-score 0.48

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 Q04IN8
Elsewhere: RCSB PDB 5LY6 · PDBe 5LY6 · UniProt Q04IN8

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