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Cryo-EM structure of the yeast mitochondrial SAM-TOM40/TOM5/TOM6 complex at 3.0 ångström

Analyse Cryo-EM structure of the yeast mitochondrial SAM-TOM40/TOM5/TOM6 complex at 3.0… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7E4I
Type: protein
Length: 1,426 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting assembly machinery 50 kda subunit; Sorting assembly machinery 35 kda subunit…
UniProt: P53969, P14693, P50110, P23644, P80967, P33448
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 6 distinct chains · 33% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Sorting assembly machinery 50 kda subunit	protein	439	12% helix, 50% strand	P53969
B	Sorting assembly machinery 35 kda subunit	protein	317	49% helix, 10% strand	P14693
C	Sorting assembly machinery 37 kda subunit	protein	291	62% helix, 5% strand	P50110
D	Mitochondrial import receptor subunit TOM40	protein	307	7% helix, 61% strand	P23644
E	Mitochondrial import receptor subunit TOM5	protein	37	95% helix, 0% strand	P80967
F	Mitochondrial import receptor subunit TOM6	protein	35	74% helix, 0% strand	P33448

Pockets

20 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	1036	0.86	0.87	91	empty
2	382	0.78	0.88	39	empty
3	900	0.74	0.78	82	empty
4	428	0.65	0.78	56	empty
5	182	0.65	0.85	34	empty

Interfaces

6 interfaces between chains.

A–B · 2177 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1542 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 851 Å² buried · 3 hydrogen bonds · protein-protein
D–F · 829 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 648 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7E4I · Cryo-EM structure of the yeast mitochondrial SAM-Tom40/Tom5/Tom6 complex at 3.0 angstrom · the same entry in another collection · chain F against F, TM-score 1.00
P50110 · AlphaFold monomer V2.0 prediction for sorting assembly machinery 37 kda subunit (P50110) · a predicted model of the same protein · chain C against A, TM-score 0.96
P23644 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM40 (P23644) · a predicted model of the same protein · chain D against A, TM-score 0.96
P53969 · AlphaFold monomer V2.0 prediction for sorting assembly machinery 50 kda subunit (P53969) · a predicted model of the same protein · chain A against A, TM-score 0.91
P14693 · AlphaFold monomer V2.0 prediction for sorting assembly machinery 35 kda subunit (P14693) · a predicted model of the same protein · chain B against A, TM-score 0.90
P33448 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM6 (P33448) · a predicted model of the same protein · chain F against A, TM-score 0.71
P80967 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM5 (P80967) · a predicted model of the same protein · chain E 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 P53969
Every structure of UniProt P14693
Every structure of UniProt P50110
Every structure of UniProt P23644
Every structure of UniProt P80967
Every structure of UniProt P33448
Elsewhere: RCSB PDB 7E4I · PDBe 7E4I · UniProt P53969 · UniProt P14693 · UniProt P50110 · UniProt P23644 · UniProt P80967 · UniProt P33448

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