MolNFT v1 · #140250 · protein

Cryo-EM structure of mscs channel, ynai

5Y4O · Low conductance mechanosensitive channel ynai: “Cryo-EM structure of mscs channel, ynai”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #140250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Y4O
Type: protein
Length: 1,561 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Low conductance mechanosensitive channel ynai
UniProt: P0AEB6
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Low conductance mechanosensitive channel ynai	protein	223	48% helix, 13% strand	P0AEB6

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1194	0.81	0.83	68	empty
2	99	0.74	0.95	18	empty
3	99	0.74	0.95	18	empty
4	96	0.73	0.95	18	empty
5	99	0.73	0.94	18	empty

Interfaces

14 interfaces between chains.

B–C · 3002 Å² buried · 28 hydrogen bonds · protein-protein
A–B · 2994 Å² buried · 28 hydrogen bonds · protein-protein
D–E · 2991 Å² buried · 27 hydrogen bonds · protein-protein
E–F · 2985 Å² buried · 27 hydrogen bonds · protein-protein
F–G · 2975 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

5Y4O · Cryo-EM structure of MscS channel, YnaI · the same entry in another collection · chain G against G, TM-score 1.00
P0AEB6 · AlphaFold monomer V2.0 prediction for low conductance mechanosensitive channel ynai… · a predicted model of the same protein · chain A against A, TM-score 0.86

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 P0AEB6
Elsewhere: RCSB PDB 5Y4O · PDBe 5Y4O · UniProt P0AEB6

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