Research workbench
SEC61 in the canine ribosome-channel complex from the endoplasmic reticulum
Analyse SEC61 in the canine ribosome-channel complex from the endoplasmic reticulum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DKN
- Type
- protein + RNA
- Length
- 596 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*GP*C)-3'); RNA (5'…
- Pockets
- 12 · best druggability 0.74
Structure
electron microscopy · 6 distinct chains · 61% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | RNA (5'- R(P*CP*GP*UP*GP*CP*CP*AP*AP*GP*CP*UP*GP*CP*GP*AP*UP*AP*AP*GP*C)-3') | rna | 20 | — | — |
| E | RNA (5'- R(P*AP*GP*CP*CP*GP*CP*AP*CP*GP*GP*AP*GP*GP*CP*GP*AP*A)-3') | rna | 17 | — | — |
| F | RNA (32-mer) | rna | 32 | — | — |
| A | Preprotein translocase subunit secy | protein | 430 | 59% helix, 1% strand | — |
| B | Preprotein translocase subunit sece | protein | 65 | 83% helix, 0% strand | — |
| C | Preprotein translocase subunit secg | protein | 32 | 53% helix, 3% strand | — |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.74 | 0.79 | 80 | empty |
| 2 | 690 | 0.68 | 0.76 | 77 | empty |
| 3 | 414 | 0.68 | 0.80 | 46 | empty |
| 4 | 294 | 0.57 | 0.76 | 34 | empty |
| 5 | 317 | 0.55 | 0.76 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1493 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1337 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 343 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- F–A · 223 Ų buried · 4 hydrogen bonds · protein-nucleic
- E–A · 188 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3DKN · Sec61 in the Canine ribosome-channel complex from the endoplasmic reticulum · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3DKN · PDBe 3DKN
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