Research workbench
Cryo-EM structure of the mitochondrial tom complex from yeast (tetramer)
Analyse Cryo-EM structure of the mitochondrial tom complex from yeast (tetramer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 6 hydrogen bonds · protein-protein
- I–M · 1058 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 1050 Ų buried · 7 hydrogen bonds · protein-protein
- a–e · 1042 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 871 Ų 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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