MolNFT v1 · #110799 · protein

Structure of an archaeal mechanosensitive channel in closed state

4Y7K · Large conductance mechanosensitive channel protein…: “Structure of an archaeal mechanosensitive channel in closed state”. X-ray diffraction, 18 pockets (best druggability 0.78). MolNFT v1 #110799 on GenesisL1: 3D structure, binding…

PDB: 4Y7K
Type: protein
Length: 1,216 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
Pockets: 18 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 62% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	250	60% helix, 13% strand	Q8TNK0, Q58584
B	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	241	64% helix, 13% strand	Q8TNK0, Q58584
C	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	241	63% helix, 13% strand	Q8TNK0, Q58584
D, E	Large conductance mechanosensitive channel protein, riboflavin synthase	protein	242	62% helix, 13% strand	Q8TNK0, Q58584

Pockets

18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	935	0.78	0.80	78	empty
2	539	0.72	0.80	48	empty
3	526	0.68	0.78	48	empty
4	498	0.68	0.78	46	empty
5	468	0.68	0.79	46	empty

Interfaces

10 interfaces between chains.

A–B · 2457 Å² buried · 23 hydrogen bonds · protein-protein
A–E · 2358 Å² buried · 30 hydrogen bonds · protein-protein
D–E · 2301 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 2267 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 2262 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

4Y7K · Structure of an archaeal mechanosensitive channel in closed 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 A against A, TM-score 0.60

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 4Y7K · PDBe 4Y7K · UniProt Q8TNK0 · UniProt Q58584

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