Research workbench
Cryo-EM structure of the human Sec61 complex inhibited by decatransin
Analyse Cryo-EM structure of the human Sec61 complex inhibited by decatransin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DNY
- Type
- protein
- Length
- 559 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Protein transport protein Sec61 subunit alpha isoform 1; Protein transport protein Sec61…
- UniProt
- P61619, P60059, P60468
- Pockets
- 5 · best druggability 0.68
Structure
electron microscopy · resolution 2.85 · 4 distinct chains · 67% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein Sec61 subunit alpha isoform 1 | protein | 456 | 64% helix, 6% strand | P61619 |
| B | Protein transport protein Sec61 subunit gamma | protein | 61 | 87% helix, 2% strand | P60059 |
| C | Protein transport protein Sec61 subunit beta | protein | 32 | 81% helix, 6% strand | P60468 |
| D | Decatransin peptide inhibitor | protein | 10 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.68 | 0.77 | 62 | empty |
| 2 | 615 | 0.66 | 0.75 | 61 | empty |
| 3 | 143 | 0.59 | 0.83 | 20 | empty |
| 4 | 112 | 0.41 | 0.75 | 18 | empty |
| 5 | 66 | 0.30 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1823 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1012 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 820 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 212 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 modified (nonstandard).
Compared structures
- P61619 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P60059 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 subunit gamma… · a predicted model of the same protein · chain B against A, TM-score 0.91
- P60468 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 subunit beta… · a predicted model of the same protein · chain C against A, TM-score 0.70
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 P61619
- Every structure of UniProt P60059
- Every structure of UniProt P60468
- Elsewhere: RCSB PDB 8DNY · PDBe 8DNY · UniProt P61619 · UniProt P60059 · UniProt P60468
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