Research workbench

Cryo-EM structure of arabidopsis thaliana MSL1 A320V

Analyse Cryo-EM structure of arabidopsis thaliana MSL1 A320V in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VXN
Type: protein
Length: 1,862 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mechanosensitive ion channel protein 1, mitochondrial
UniProt: Q8VZL4
Ligands: D12
Pockets: 20 · best druggability 0.74

Structure

electron microscopy · 1 distinct chain · 52% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Mechanosensitive ion channel protein 1, mitochondrial	protein	266	52% helix, 22% strand	Q8VZL4

Ligands and binding sites

D12 · Dodecane · ligand · 7 copies · chains A, B, C, D, E, F, G

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1023	0.74	0.77	91	D12
2	1097	0.74	0.77	91	D12
3	1137	0.74	0.77	88	D12
4	583	0.74	0.81	55	D12
5	1051	0.73	0.76	93	D12

Interfaces

14 interfaces between chains.

F–G · 2258 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 2258 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 2257 Å² buried · 9 hydrogen bonds · protein-protein
A–G · 2196 Å² buried · 6 hydrogen bonds · protein-protein
D–E · 2189 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6VXN · Cryo-EM structure of Arabidopsis thaliana MSL1 A320V · the same entry in another collection · chain G against G, TM-score 1.00
Q8VZL4 · AlphaFold monomer V2.0 prediction for mechanosensitive ion channel protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.66

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 Q8VZL4
Elsewhere: RCSB PDB 6VXN · PDBe 6VXN · UniProt Q8VZL4

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