Research workbench

Structure of an archaeal mechanosensitive channel in expanded state

Analyse Structure of an archaeal mechanosensitive channel in expanded state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Y7J
Type: protein
Length: 1,170 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Large conductance mechanosensitive channel protein, riboflavin synthase
UniProt: Q8TNK0, Q58584
Ligands: BNG
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	241	56% helix, 3% strand	Q8TNK0, Q58584
B	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	230	54% helix, 3% strand	Q8TNK0, Q58584
C	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	234	54% helix, 7% strand	Q8TNK0, Q58584
D	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	234	56% helix, 9% strand	Q8TNK0, Q58584
E	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	231	58% helix, 6% strand	Q8TNK0, Q58584

Ligands and binding sites

BNG · nonyl beta-D-glucopyranoside · ligand · chains A, B, D, E

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1066	0.78	0.79	114	empty
2	275	0.76	0.88	40	empty
3	795	0.73	0.78	100	empty
4	379	0.72	0.84	42	empty
5	384	0.71	0.83	35	empty

Interfaces

10 interfaces between chains.

B–C · 2127 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 2046 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 1964 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1964 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 1868 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4Y7J · Structure of an archaeal mechanosensitive channel in expanded state · the same entry in another collection · chain E against E, TM-score 1.00
Q58584 · AlphaFold monomer V2.0 prediction for riboflavin synthase (Q58584) · a predicted model of the same protein · chain B against A, TM-score 0.65

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 Q8TNK0
Every structure of UniProt Q58584
Elsewhere: RCSB PDB 4Y7J · PDBe 4Y7J · UniProt Q8TNK0 · UniProt Q58584

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