Research workbench

Cryo-EM structure of the TIM22 complex from yeast

Analyse Cryo-EM structure of the TIM22 complex from yeast in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LO8
Type: protein
Length: 997 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mitochondrial import inner membrane translocase subunit TIM22; Mitochondrial import inner…
UniProt: Q12328, P47045, P33421, Q08749, O74700, P32830, P87108
Pockets: 15 · best druggability 0.81

Structure

electron microscopy · 9 distinct chains · 74% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitochondrial import inner membrane translocase subunit TIM22	protein	129	75% helix, 0% strand	Q12328
B	Mitochondrial import inner membrane translocase subunit TIM54	protein	176	61% helix, 8% strand	P47045
C	Succinate dehydrogenase [ubiquinone] cytochrome B subunit, mitochondrial	protein	108	88% helix, 0% strand	P33421
D	Mitochondrial import inner membrane translocase subunit TIM18	protein	119	68% helix, 0% strand	Q08749
E, I	Mitochondrial import inner membrane translocase subunit TIM9	protein	80	78% helix, 0% strand	O74700
F	Mitochondrial import inner membrane translocase subunit TIM12	protein	84	77% helix, 0% strand	P32830
G	Mitochondrial import inner membrane translocase subunit TIM9	protein	74	81% helix, 0% strand	O74700
H	Mitochondrial import inner membrane translocase subunit TIM10	protein	74	77% helix, 0% strand	P87108
J	Mitochondrial import inner membrane translocase subunit TIM10	protein	73	74% helix, 1% strand	P87108

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	444	0.81	0.88	42	empty
2	740	0.72	0.77	54	empty
3	1099	0.69	0.74	85	empty
4	150	0.60	0.83	30	empty
5	464	0.60	0.74	38	empty

Interfaces

20 interfaces between chains.

C–D · 2069 Å² buried · 10 hydrogen bonds · protein-protein
F–G · 1931 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1731 Å² buried · 13 hydrogen bonds · protein-protein
I–J · 1619 Å² buried · 11 hydrogen bonds · protein-protein
G–H · 1481 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide (disulfide).

Compared structures

6LO8 · Cryo-EM structure of the TIM22 complex from yeast · the same entry in another collection · chain J against J, TM-score 1.00
P47045 · AlphaFold monomer V2.0 prediction for mitochondrial import inner membrane translocase… · a predicted model of the same protein · chain B against A, TM-score 0.96
O74700 · AlphaFold monomer V2.0 prediction for mitochondrial import inner membrane translocase… · a predicted model of the same protein · chain G against A, TM-score 0.93

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 Q12328
Every structure of UniProt P47045
Every structure of UniProt P33421
Every structure of UniProt Q08749
Every structure of UniProt O74700
Every structure of UniProt P32830
Every structure of UniProt P87108
Elsewhere: RCSB PDB 6LO8 · PDBe 6LO8 · UniProt Q12328 · UniProt P47045 · UniProt P33421 · UniProt Q08749 · UniProt O74700 · UniProt P32830 · UniProt P87108

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