Research workbench
Cryoem structure of HRD1-USA1/DER1/HRD3 of the flipped topology
Analyse Cryoem structure of HRD1-USA1/DER1/HRD3 of the flipped topology in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VK0
- Type
- protein
- Length
- 1,160 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- U1 SNP1-associating protein 1; Degradation in the endoplasmic reticulum protein 1…
- EC
- 2.3.2.27
- UniProt
- Q03714, P38307, Q05787, Q08109
- Pockets
- 20 · best druggability 0.69
Structure
electron microscopy · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | U1 SNP1-associating protein 1 | protein | 97 | 65% helix, 0% strand | Q03714 |
| C | Degradation in the endoplasmic reticulum protein 1 | protein | 180 | 65% helix, 1% strand | P38307 |
| A | Erad-associated E3 ubiquitin-protein ligase component HRD3 | protein | 603 | 65% helix, 0% strand | Q05787 |
| B | Erad-associated E3 ubiquitin-protein ligase HRD1 (EC 2.3.2.27) | protein | 280 | 86% helix, 0% strand | Q08109 |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.69 | 0.76 | 58 | empty |
| 2 | 513 | 0.68 | 0.78 | 56 | empty |
| 3 | 396 | 0.68 | 0.80 | 59 | empty |
| 4 | 428 | 0.67 | 0.79 | 42 | empty |
| 5 | 395 | 0.67 | 0.79 | 50 | empty |
Interfaces
4 interfaces between chains.
- D–C · 1583 Ų buried · 5 hydrogen bonds · protein-protein
- D–B · 723 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 716 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 87 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VK0 · CryoEM structure of Hrd1-Usa1/Der1/Hrd3 of the flipped topology · the same entry in another collection · chain A against A, 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 0.83
- 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 0.37
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 Q03714
- Every structure of UniProt P38307
- Every structure of UniProt Q05787
- Every structure of UniProt Q08109
- Elsewhere: RCSB PDB 6VK0 · PDBe 6VK0 · UniProt Q03714 · UniProt P38307 · UniProt Q05787 · UniProt Q08109
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