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Cryo-EM structure of the mitochondrial tom complex from yeast (dimer)

Analyse Cryo-EM structure of the mitochondrial tom complex from yeast (dimer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UCU
Type: protein
Length: 958 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial import receptor subunit TOM40; Mitochondrial import receptor subunit TOM22…
UniProt: P23644, P49334, P80967, P33448, P53507
Pockets: 17 · best druggability 0.84

Structure

electron microscopy · 5 distinct chains · 34% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I	Mitochondrial import receptor subunit TOM40	protein	307	7% helix, 59% strand	P23644
B, J	Mitochondrial import receptor subunit TOM22	protein	50	96% helix, 0% strand	P49334
C, K	Mitochondrial import receptor subunit TOM5	protein	37	95% helix, 0% strand	P80967
D, L	Mitochondrial import receptor subunit TOM6	protein	35	71% helix, 0% strand	P33448
E, M	Mitochondrial import receptor subunit TOM7	protein	50	72% helix, 0% strand	P53507

Ligands and binding sites

LMT · Dodecyl-beta-D-maltoside · additive · 60 copies · chains A, B, D, I, E, J, C, M, L, K

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

Pockets

17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	988	0.84	0.84	69	LMT
2	262	0.55	0.77	32	LMT
3	144	0.48	0.77	20	LMT
4	113	0.42	0.77	19	empty
5	175	0.42	0.73	26	LMT

Interfaces

14 interfaces between chains.

I–M · 1051 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 1047 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 890 Å² buried · 2 hydrogen bonds · protein-protein
I–K · 881 Å² buried · 1 hydrogen bond · protein-protein
I–L · 873 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6UCU · Cryo-EM structure of the mitochondrial TOM complex from yeast (dimer) · the same entry in another collection · chain M against M, 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 0.98
P49334 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM22 (P49334) · a predicted model of the same protein · chain B against A, TM-score 0.83

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

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