MolNFT v1 · #165999 · protein

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

6UCV · Mitochondrial import receptor subunit TOM40: “Cryo-EM structure of the mitochondrial tom complex from yeast (tetramer)”. Electron microscopy, 1 ligand (MC3), 20 pockets (best druggability 0.84). MolNFT v1 #165999 on GenesisL1: 3D…

PDB: 6UCV
Type: protein
Length: 1,947 residues
Chains: 20
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
Ligands: MC3
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 11 distinct chains · 24% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mitochondrial import receptor subunit TOM40	protein	313	8% helix, 58% strand	P23644
B, j	Mitochondrial import receptor subunit TOM22	protein	50	96% helix, 0% strand	P49334
C, K, c, k	Mitochondrial import receptor subunit TOM5	protein	37	95% helix, 0% strand	P80967
D, l	Mitochondrial import receptor subunit TOM6	protein	35	74% helix, 0% strand	P33448
E, M, e, m	Mitochondrial import receptor subunit TOM7	protein	50	70% helix, 0% strand	P53507
I	Mitochondrial import receptor subunit TOM40	protein	311	8% helix, 58% strand	P23644
J	Mitochondrial import receptor subunit TOM22	protein	55	96% helix, 0% strand	P49334
L, d	Mitochondrial import receptor subunit TOM6	protein	37	70% helix, 0% strand	P33448
a	Mitochondrial import receptor subunit TOM40	protein	317	9% helix, 56% strand	P23644
b	Mitochondrial import receptor subunit TOM22	protein	52	96% helix, 0% strand	P49334
i	Mitochondrial import receptor subunit TOM40	protein	307	7% helix, 59% strand	P23644

Ligands and binding sites

MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 2 copies · chains A, B, I, J, a, b, i, j

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	906	0.84	0.86	68	MC3
2	980	0.84	0.85	79	MC3
3	1153	0.74	0.77	89	empty
4	269	0.54	0.76	42	empty
5	164	0.52	0.78	17	empty

Interfaces

35 interfaces between chains.

i–m · 1061 Å² buried · 6 hydrogen bonds · protein-protein
I–M · 1058 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 1050 Å² buried · 7 hydrogen bonds · protein-protein
a–e · 1042 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 871 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6UCV · Cryo-EM structure of the mitochondrial TOM complex from yeast (tetramer) · the same entry in another collection · chain E against E, TM-score 1.00

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 6UCV · PDBe 6UCV · UniProt P23644 · UniProt P49334 · UniProt P80967 · UniProt P33448 · UniProt P53507

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