Research workbench
Cryo-EM of the SEC61-complex bound to the 80S ribosome translating a membrane-inserting substrate
Analyse Cryo-EM of the SEC61-complex bound to the 80S ribosome translating a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CG6
- Type
- protein
- Length
- 567 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein transport protein SEC61 subunit alpha isoform 1; Protein transport protein SEC61…
- UniProt
- P38377, P60058, P60467
- Pockets
- 7 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 54% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 subunit alpha isoform 1 | protein | 452 | 51% helix, 0% strand | P38377 |
| B | Protein transport protein SEC61 subunit gamma | protein | 62 | 77% helix, 0% strand | P60058 |
| C | Protein transport protein SEC61 subunit beta | protein | 36 | 44% helix, 0% strand | P60467 |
| D | Peptide | protein | 17 | 88% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.85 | 0.86 | 102 | empty |
| 2 | 1020 | 0.75 | 0.78 | 100 | empty |
| 3 | 119 | 0.73 | 0.93 | 30 | empty |
| 4 | 360 | 0.64 | 0.79 | 42 | empty |
| 5 | 186 | 0.57 | 0.80 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1600 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 947 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 617 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4CG6 · Cryo-em of the Sec61-complex bound to the 80s ribosome translating a membrane-inserting… · the same entry in another collection · chain A against A, TM-score 1.00
- P38377 · 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 0.71
- P60058 · 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 0.58
- P60467 · 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 0.54
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 P38377
- Every structure of UniProt P60058
- Every structure of UniProt P60467
- Elsewhere: RCSB PDB 4CG6 · PDBe 4CG6 · UniProt P38377 · UniProt P60058 · UniProt P60467
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