MolNFT v1 · #136921 · protein
Cryo-EM structure of erad-associated E3 ubiquitin-protein ligase component HRD3
5V7V: “Cryo-EM structure of erad-associated E3 ubiquitin-protein ligase component HRD3”. Electron microscopy, 2 ligands (NAG, BMA), 9 pockets (best druggability 0.73). MolNFT v1 #136921 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5V7V
- Type
- protein
- Length
- 613 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erad-associated E3 ubiquitin-protein ligase component HRD3
- UniProt
- Q05787
- Ligands
- NAG, BMA
- Pockets
- 9 · best druggability 0.73
Structure
electron microscopy · 1 distinct chain · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erad-associated E3 ubiquitin-protein ligase component HRD3 | protein | 613 | 62% helix, 0% strand | Q05787 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.73 | 0.82 | 57 | NAG |
| 2 | 791 | 0.71 | 0.77 | 65 | empty |
| 3 | 249 | 0.62 | 0.81 | 42 | empty |
| 4 | 171 | 0.61 | 0.83 | 39 | empty |
| 5 | 361 | 0.59 | 0.76 | 47 | empty |
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 5V7V · Cryo-EM structure of ERAD-associated E3 ubiquitin-protein ligase component HRD3 · 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 0.97
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 Q05787
- Elsewhere: RCSB PDB 5V7V · PDBe 5V7V · UniProt Q05787
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