Research workbench
The cryo-EM structure of the erad retrotranslocation channel formed by human derlin-1
Analyse The cryo-EM structure of the erad retrotranslocation channel formed by human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CZB
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Derlin-1
- UniProt
- Q9BUN8
- Pockets
- 17 · best druggability 0.47
Structure
electron microscopy · 1 distinct chain · 55% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Derlin-1 | protein | 194 | 55% helix, 0% strand | Q9BUN8 |
Pockets
17 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.47 | 0.77 | 22 | empty |
| 2 | 133 | 0.45 | 0.76 | 17 | empty |
| 3 | 143 | 0.45 | 0.76 | 21 | empty |
| 4 | 122 | 0.44 | 0.77 | 21 | empty |
| 5 | 98 | 0.43 | 0.78 | 11 | empty |
Interfaces
4 interfaces between chains.
- C–D · 409 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 408 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 329 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 329 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7CZB · The cryo-EM structure of the ERAD retrotranslocation channel formed by human Derlin-1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BUN8 · AlphaFold monomer V2.0 prediction for derlin-1 (Q9BUN8) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 Q9BUN8
- Elsewhere: RCSB PDB 7CZB · PDBe 7CZB · UniProt Q9BUN8
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