Research workbench
Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at 3.0 angstrom
Analyse Cryo-EM structure of the yeast mitochondrial SAM-Tom40 complex at 3.0 angstrom in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E4H
- Type
- protein
- Length
- 1,354 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.01
- Source
- Saccharomyces cerevisiae S288c
- Molecule
- Sorting assembly machinery 50 kDa subunit; Sorting assembly machinery 35 kDa subunit…
- UniProt
- P53969, P14693, P50110, P23644
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · resolution 3.01 · 4 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorting assembly machinery 50 kDa subunit | protein | 439 | 11% helix, 50% strand | P53969 |
| B | Sorting assembly machinery 35 kDa subunit | protein | 317 | 43% helix, 10% strand | P14693 |
| C | Sorting assembly machinery 37 kDa subunit | protein | 291 | 60% helix, 6% strand | P50110 |
| D | Mitochondrial import receptor subunit TOM40 | protein | 307 | 7% helix, 57% strand | P23644 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.86 | 0.87 | 119 | empty |
| 2 | 467 | 0.79 | 0.86 | 38 | empty |
| 3 | 1193 | 0.72 | 0.76 | 86 | empty |
| 4 | 612 | 0.68 | 0.77 | 67 | empty |
| 5 | 465 | 0.64 | 0.77 | 53 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2139 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1459 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 512 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 357 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7E4H · Cryo-EM structure of the yeast mitochondrial SAM-TOM40 complex at 3.0 ångström · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.97
- 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
- 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
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
- Elsewhere: RCSB PDB 7E4H · PDBe 7E4H · UniProt P53969 · UniProt P14693 · UniProt P50110 · UniProt P23644
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