MolNFT v1 · #165998 · protein
Cryo-EM structure of the mitochondrial tom complex from yeast (dimer)
6UCU · Mitochondrial import receptor subunit TOM40: “Cryo-EM structure of the mitochondrial tom complex from yeast (dimer)”. Electron microscopy, 17 pockets (best druggability 0.84). MolNFT v1 #165998 on GenesisL1: 3D structure, binding…
- 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.
| Volume (ų) | 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 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1047 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 890 Ų buried · 2 hydrogen bonds · protein-protein
- I–K · 881 Ų buried · 1 hydrogen bond · protein-protein
- I–L · 873 Ų 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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