Research workbench
Cryoem structure of the erad-associated E3 ubiquitin-protein ligase HRD1
Analyse Cryoem structure of the erad-associated E3 ubiquitin-protein ligase HRD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V6P
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erad-associated E3 ubiquitin-protein ligase HRD1
- EC
- 2.3.2.27
- UniProt
- Q08109
- Pockets
- 5 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Erad-associated E3 ubiquitin-protein ligase HRD1 (EC 2.3.2.27) | protein | 270 | 88% helix, 0% strand | Q08109 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.86 | 0.88 | 95 | empty |
| 2 | 563 | 0.75 | 0.82 | 47 | empty |
| 3 | 486 | 0.73 | 0.82 | 34 | empty |
| 4 | 153 | 0.56 | 0.81 | 22 | empty |
| 5 | 52 | 0.31 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1812 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V6P · CryoEM structure of the ERAD-associated E3 ubiquitin-protein ligase HRD1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q08109 · AlphaFold monomer V2.0 prediction for erad-associated E3 ubiquitin- protein ligase HRD1… · a predicted model of the same protein · chain A 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 Q08109
- Elsewhere: RCSB PDB 5V6P · PDBe 5V6P · UniProt Q08109
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