MolNFT v1 · #167412 · protein
Cryo-EM structure of HRD1/HRD3 monomer
6VJY · Erad-associated E3 ubiquitin-protein ligase HRD1: “Cryo-EM structure of HRD1/HRD3 monomer”. Electron microscopy, 16 pockets (best druggability 0.70). MolNFT v1 #167412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VJY
- Type
- protein
- Length
- 883 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erad-associated E3 ubiquitin-protein ligase HRD1; Erad-associated E3 ubiquitin-protein…
- EC
- 2.3.2.27
- UniProt
- Q08109, Q05787
- Pockets
- 16 · best druggability 0.70
Structure
electron microscopy · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Erad-associated E3 ubiquitin-protein ligase HRD1 (EC 2.3.2.27) | protein | 280 | 85% helix, 0% strand | Q08109 |
| A | Erad-associated E3 ubiquitin-protein ligase component HRD3 | protein | 603 | 65% helix, 0% strand | Q05787 |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.70 | 0.77 | 64 | empty |
| 2 | 505 | 0.70 | 0.80 | 56 | empty |
| 3 | 442 | 0.67 | 0.79 | 45 | empty |
| 4 | 92 | 0.57 | 0.85 | 14 | empty |
| 5 | 194 | 0.56 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- B–A · 702 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6VJY · Cryo-EM structure of Hrd1/Hrd3 monomer · the same entry in another collection · chain B against B, 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 0.93
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
- Every structure of UniProt Q05787
- Elsewhere: RCSB PDB 6VJY · PDBe 6VJY · UniProt Q08109 · UniProt Q05787
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