Research workbench
Crystal structure of rat TOM20-aldh presequence complex: a complex (FORM2) between TOM20 and a disulfide-bridged presequence peptide containing D-cys and L-cys at the I and I+3 positions.
Analyse Crystal structure of rat TOM20-aldh presequence complex: a complex (FORM2)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AX3
- Type
- protein
- Length
- 312 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial import receptor subunit TOM20 homolog; Aldehyde dehydrogenase, mitochondrial
- UniProt
- Q62760, P11884
- Ligands
- NH2
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 83% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mitochondrial import receptor subunit TOM20 homolog | protein | 66 | 85% helix, 0% strand | Q62760 |
| B, D, F, H | Aldehyde dehydrogenase, mitochondrial | protein | 11 | 73% helix, 0% strand | P11884 |
| E, G | Mitochondrial import receptor subunit TOM20 homolog | protein | 68 | 84% helix, 0% strand | Q62760 |
Ligands and binding sites
- NH2 · Amino group · ion · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.51 | 0.73 | 46 | empty |
| 2 | 155 | 0.46 | 0.76 | 28 | empty |
| 3 | 153 | 0.41 | 0.73 | 17 | empty |
| 4 | 97 | 0.36 | 0.74 | 16 | empty |
Interfaces
8 interfaces between chains.
- C–D · 522 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 511 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 498 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 487 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 449 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 d-amino, 4 disulfide (D-amino acid, disulfide).
Compared structures
- 3AX3 · Crystal structure of rat TOM20-ALDH presequence complex: a complex (form2) between Tom20… · the same entry in another collection · chain H against H, TM-score 1.00
- Q62760 · AlphaFold monomer V2.0 prediction for mitochondrial import receptor subunit TOM20 homolog… · a predicted model of the same protein · chain A against A, TM-score 0.86
- P11884 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, mitochondrial (P11884) · a predicted model of the same protein · chain F against A, TM-score 0.74
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 Q62760
- Every structure of UniProt P11884
- Elsewhere: RCSB PDB 3AX3 · PDBe 3AX3 · UniProt Q62760 · UniProt P11884
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