MolNFT v1 · #167856 · protein

Cryo-EM structure of arabidopsis thaliana MSL1

6VXM · Mechanosensitive ion channel protein 1, mitochondrial: “Cryo-EM structure of arabidopsis thaliana MSL1”. Electron microscopy, 1 ligand (LFA), 20 pockets (best druggability 0.73). MolNFT v1 #167856 on GenesisL1: 3D structure, binding…

PDB: 6VXM
Type: protein
Length: 1,939 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mechanosensitive ion channel protein 1, mitochondrial
UniProt: Q8VZL4
Ligands: LFA
Pockets: 20 · best druggability 0.73

Structure

electron microscopy · 1 distinct chain · 53% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Mechanosensitive ion channel protein 1, mitochondrial	protein	277	53% helix, 21% strand	Q8VZL4

Ligands and binding sites

LFA · Eicosane · ligand · 21 copies · chains F, G, A, B, C, 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1032	0.73	0.76	136	LFA
2	615	0.64	0.74	48	empty
3	377	0.60	0.77	59	empty
4	58	0.59	0.91	19	empty
5	65	0.58	0.89	19	empty

Interfaces

7 interfaces between chains.

A–G · 2380 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 2378 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 2375 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 2374 Å² buried · 13 hydrogen bonds · protein-protein
D–E · 2372 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

6VXM · Cryo-EM structure of Arabidopsis thaliana MSL1 · 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 0.97

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 6VXM · PDBe 6VXM · UniProt Q8VZL4

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