Research workbench
Cryo-EM of the SEC61-complex bound to the 80S ribosome translating a secretory substrate
Analyse Cryo-EM of the SEC61-complex bound to the 80S ribosome translating a secretory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CG5
- Type
- protein
- Length
- 550 residues
- Chains
- 3
- 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
- 10 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 57% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein transport protein SEC61 subunit alpha isoform 1 | protein | 452 | 56% helix, 0% strand | P38377 |
| B | Protein transport protein SEC61 subunit gamma | protein | 62 | 74% helix, 0% strand | P60058 |
| C | Protein transport protein SEC61 subunit beta | protein | 36 | 33% helix, 0% strand | P60467 |
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.84 | 0.88 | 83 | empty |
| 2 | 199 | 0.72 | 0.88 | 33 | empty |
| 3 | 320 | 0.72 | 0.84 | 37 | empty |
| 4 | 120 | 0.68 | 0.89 | 28 | empty |
| 5 | 106 | 0.65 | 0.89 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1535 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 984 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4CG5 · Cryo-EM of the Sec61-complex bound to the 80S ribosome translating a secretory substrate · 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 0.72
- 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 0.59
- 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 0.42
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 4CG5 · PDBe 4CG5 · UniProt P38377 · UniProt P60058 · UniProt P60467
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