MolNFT v1 · #153723 · protein
Cryo-EM structure of the translocator of the outer mitochondrial membrane
6JNF · Mitochondrial import receptor subunit TOM40: “Cryo-EM structure of the translocator of the outer mitochondrial membrane”. Electron microscopy, 1 ligand (46E), 15 pockets (best druggability 0.85). MolNFT v1 #153723 on GenesisL1: 3D…
- PDB
- 6JNF
- Type
- protein
- Length
- 924 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial import receptor subunit TOM40; Mitochondrial import receptor subunit TOM7…
- UniProt
- P23644, P53507, P49334, P80967, P33448
- Ligands
- 46E
- Pockets
- 15 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Mitochondrial import receptor subunit TOM40 | protein | 306 | 3% helix, 42% strand | P23644 |
| B, G | Mitochondrial import receptor subunit TOM7 | protein | 41 | 49% helix, 0% strand | P53507 |
| C, H | Mitochondrial import receptor subunit TOM22 | protein | 44 | 52% helix, 0% strand | P49334 |
| D, I | Mitochondrial import receptor subunit TOM5 | protein | 34 | 76% helix, 0% strand | P80967 |
| E, J | Mitochondrial import receptor subunit TOM6 | protein | 37 | 62% helix, 0% strand | P33448 |
Ligands and binding sites
- 46E · (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate · ligand · chains A, C, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.85 | 0.86 | 77 | 46E |
| 2 | 105 | 0.55 | 0.84 | 21 | empty |
| 3 | 67 | 0.55 | 0.88 | 15 | empty |
| 4 | 136 | 0.45 | 0.76 | 20 | empty |
| 5 | 118 | 0.41 | 0.76 | 18 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1099 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 1091 Ų buried · 5 hydrogen bonds · protein-protein
- F–I · 822 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 807 Ų buried · 0 hydrogen bonds · protein-protein
- F–J · 801 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6JNF · Cryo-EM structure of the translocator of the outer mitochondrial membrane · the same entry in another collection · chain J against J, 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 0.95
- P49334 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM22 (P49334) · a predicted model of the same protein · chain C against A, TM-score 0.69
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 P53507
- Every structure of UniProt P49334
- Every structure of UniProt P80967
- Every structure of UniProt P33448
- Elsewhere: RCSB PDB 6JNF · PDBe 6JNF · UniProt P23644 · UniProt P53507 · UniProt P49334 · UniProt P80967 · UniProt P33448
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