Research workbench
Cryoem structure of HRD1-USA1/DER1/HRD3 complex of the expected topology
Analyse Cryoem structure of HRD1-USA1/DER1/HRD3 complex of the expected topology in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VJZ
- Type
- protein
- Length
- 1,093 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Degradation in the endoplasmic reticulum protein 1; Erad-associated E3 ubiquitin-protein…
- EC
- 2.3.2.27
- UniProt
- P38307, Q08109, Q05787, Q03714
- Pockets
- 19 · best druggability 0.73
Structure
electron microscopy · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Degradation in the endoplasmic reticulum protein 1 | protein | 165 | 78% helix, 0% strand | P38307 |
| B | Erad-associated E3 ubiquitin-protein ligase HRD1 (EC 2.3.2.27) | protein | 280 | 86% helix, 0% strand | Q08109 |
| A | Erad-associated E3 ubiquitin-protein ligase component HRD3 | protein | 603 | 65% helix, 0% strand | Q05787 |
| D | U1 SNP1-associating protein 1 | protein | 45 | 60% helix, 0% strand | Q03714 |
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.73 | 0.78 | 79 | empty |
| 2 | 604 | 0.73 | 0.80 | 53 | empty |
| 3 | 497 | 0.69 | 0.79 | 51 | empty |
| 4 | 644 | 0.69 | 0.77 | 54 | empty |
| 5 | 261 | 0.67 | 0.82 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–A · 695 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 359 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 350 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VJZ · CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected topology · the same entry in another collection · chain D against D, TM-score 1.00
- Q05787 · AlphaFold monomer V2.0 prediction for erad-associated E3 ubiquitin- protein ligase… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q08109 · AlphaFold monomer V2.0 prediction for erad-associated E3 ubiquitin- protein ligase HRD1… · a predicted model of the same protein · chain B against A, TM-score 0.95
- P38307 · AlphaFold monomer V2.0 prediction for degradation in the endoplasmic reticulum protein 1… · a predicted model of the same protein · chain C against A, TM-score 0.87
- Q03714 · AlphaFold monomer V2.0 prediction for U1 SNP1-associating protein 1 (Q03714) · a predicted model of the same protein · chain D against A, TM-score 0.50
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 P38307
- Every structure of UniProt Q08109
- Every structure of UniProt Q05787
- Every structure of UniProt Q03714
- Elsewhere: RCSB PDB 6VJZ · PDBe 6VJZ · UniProt P38307 · UniProt Q08109 · UniProt Q05787 · UniProt Q03714
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