Research workbench
The structure of the mammalian SEC61 channel opened by a signal sequence
Analyse The structure of the mammalian SEC61 channel opened by a signal sequence in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JC2
- Type
- protein
- Length
- 514 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, Q6VMP1
- Pockets
- 11 · best druggability 0.71
Structure
electron microscopy · 4 distinct chains · 62% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Protein transport protein SEC61 subunit alpha isoform 1 | protein | 401 | 60% helix, 4% strand | P38377 |
| 2 | Protein transport protein SEC61 subunit gamma | protein | 62 | 76% helix, 0% strand | P60058 |
| w | Prolactin | protein | 19 | 74% helix, 0% strand | Q6VMP1 |
| 3 | Protein transport protein SEC61 subunit beta | protein | 32 | 56% helix, 6% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.71 | 0.75 | 101 | empty |
| 2 | 208 | 0.66 | 0.84 | 27 | empty |
| 3 | 317 | 0.55 | 0.75 | 31 | empty |
| 4 | 69 | 0.47 | 0.83 | 14 | empty |
| 5 | 82 | 0.44 | 0.80 | 18 | empty |
Interfaces
4 interfaces between chains.
- 1–2 · 1592 Ų buried · 6 hydrogen bonds · protein-protein
- 1–3 · 904 Ų buried · 5 hydrogen bonds · protein-protein
- 1–w · 871 Ų buried · 0 hydrogen bonds · protein-protein
- 2–3 · 85 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3JC2 · The structure of the mammalian Sec61 channel opened by a signal sequence · the same entry in another collection · chain 1 against 1, 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 1 against A, TM-score 0.85
- P60058 · AlphaFold monomer V2.0 prediction for protein transport protein SEC61 subunit gamma… · a predicted model of the same protein · chain 2 against A, TM-score 0.66
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 Q6VMP1
- Elsewhere: RCSB PDB 3JC2 · PDBe 3JC2 · UniProt P38377 · UniProt P60058 · UniProt Q6VMP1
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