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Cryo-EM structure of the translocator of the outer mitochondrial membrane

Analyse Cryo-EM structure of the translocator of the outer mitochondrial membrane in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JNF
Type: protein
Length: 924 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial import receptor subunit TOM40; Mitochondrial import receptor subunit TOM7…
UniProt: P23644, P53507, P49334, P80967, P33448
Ligands: 46E
Pockets: 15 · best druggability 0.85

Structure

electron microscopy · 5 distinct chains · 22% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Mitochondrial import receptor subunit TOM40	protein	306	3% helix, 42% strand	P23644
B, G	Mitochondrial import receptor subunit TOM7	protein	41	49% helix, 0% strand	P53507
C, H	Mitochondrial import receptor subunit TOM22	protein	44	52% helix, 0% strand	P49334
D, I	Mitochondrial import receptor subunit TOM5	protein	34	76% helix, 0% strand	P80967
E, J	Mitochondrial import receptor subunit TOM6	protein	37	62% helix, 0% strand	P33448

Ligands and binding sites

46E · (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate · ligand · chains A, C, F, H

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

Pockets

15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	994	0.85	0.86	77	46E
2	105	0.55	0.84	21	empty
3	67	0.55	0.88	15	empty
4	136	0.45	0.76	20	empty
5	118	0.41	0.76	18	empty

Interfaces

14 interfaces between chains.

A–B · 1099 Å² buried · 5 hydrogen bonds · protein-protein
F–G · 1091 Å² buried · 5 hydrogen bonds · protein-protein
F–I · 822 Å² buried · 1 hydrogen bond · protein-protein
A–E · 807 Å² buried · 0 hydrogen bonds · protein-protein
F–J · 801 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6JNF · Cryo-EM structure of the translocator of the outer mitochondrial membrane · the same entry in another collection · chain J against J, TM-score 1.00
P23644 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM40 (P23644) · a predicted model of the same protein · chain A against A, TM-score 0.95
P49334 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM22 (P49334) · a predicted model of the same protein · chain C against A, TM-score 0.69

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 P23644
Every structure of UniProt P53507
Every structure of UniProt P49334
Every structure of UniProt P80967
Every structure of UniProt P33448
Elsewhere: RCSB PDB 6JNF · PDBe 6JNF · UniProt P23644 · UniProt P53507 · UniProt P49334 · UniProt P80967 · UniProt P33448

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