Research workbench
Structure of hhari, a ring-ibr-ring ubiquitin ligase: autoinhibition of an ariadne-family E3 and insights into ligation mechanism
Analyse Structure of hhari, a ring-ibr-ring ubiquitin ligase: autoinhibition of an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KC9
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase ARIH1
- EC
- 6.3.2.-
- UniProt
- Q9Y4X5
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase ARIH1 (EC 6.3.2.-) | protein | 414 | 51% helix, 8% strand | Q9Y4X5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.58 | 0.79 | 32 | empty |
| 2 | 53 | 0.52 | 0.88 | 18 | empty |
| 3 | 147 | 0.50 | 0.78 | 22 | empty |
| 4 | 85 | 0.43 | 0.79 | 18 | empty |
| 5 | 54 | 0.36 | 0.79 | 14 | empty |
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4KC9 · Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y4X5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ARIH1 (Q9Y4X5) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9Y4X5
- Elsewhere: RCSB PDB 4KC9 · PDBe 4KC9 · UniProt Q9Y4X5
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