Research workbench

YNAI

Analyse YNAI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZYD
Type: protein
Length: 2,261 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Low conductance mechanosensitive channel YNAI,LOW conductance mechanosensitive channel…
UniProt: P0AEB5
Ligands: PEE
Pockets: 20 · best druggability 0.75

Structure

electron microscopy · 1 distinct chain · 58% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, C, A, B, D, F, G	Low conductance mechanosensitive channel YNAI,LOW conductance mechanosensitive channel ynai	protein	323	58% helix, 19% strand	P0AEB5

Ligands and binding sites

PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 7 copies · chains E, D, F, C, A, G, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1119	0.75	0.77	52	empty
2	414	0.62	0.76	52	empty
3	661	0.61	0.73	90	empty
4	122	0.60	0.85	21	empty
5	299	0.57	0.76	45	empty

Interfaces

14 interfaces between chains.

F–G · 3180 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 3172 Å² buried · 25 hydrogen bonds · protein-protein
C–G · 3169 Å² buried · 25 hydrogen bonds · protein-protein
C–A · 3169 Å² buried · 25 hydrogen bonds · protein-protein
E–D · 3168 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

6ZYD · YnaI · the same entry in another collection · chain G against G, TM-score 1.00
P0AEB5 · AlphaFold monomer V2.0 prediction for low conductance mechanosensitive channel ynai… · a predicted model of the same protein · chain E against A, TM-score 0.81

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 P0AEB5
Elsewhere: RCSB PDB 6ZYD · PDBe 6ZYD · UniProt P0AEB5

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