Research workbench
A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNF125
Analyse A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DKA
- Type
- protein
- Length
- 192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Homo sapiens
- Molecule
- E3 ubiquitin-protein ligase RNF125
- EC
- 6.3.2.-
- UniProt
- Q96EQ8
- Ligands
- ZN, MG, CL
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.55 · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase RNF125 (EC 6.3.2.-) | protein | 96 | 35% helix, 19% strand | Q96EQ8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.67 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 696 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DKA · A C2HC zinc finger is essential for the activity of the ring ubiquitin ligase RNF125 · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EQ8 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF125 (Q96EQ8) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q96EQ8
- Elsewhere: RCSB PDB 5DKA · PDBe 5DKA · UniProt Q96EQ8
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