Research workbench
Crystal structure of mouse Unkempt zinc fingers 1-3 (ZnF1-3), bound to RNA
Analyse Crystal structure of mouse Unkempt zinc fingers 1-3 (ZnF1-3), bound to RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ELH
- Type
- protein + RNA
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- RING finger protein unkempt homolog; RNA (5'-R(*UP*UP*AP*UP*U)-3')
- UniProt
- Q8BL48
- Ligands
- ZN, SO4
- Pockets
- 4 · best druggability 0.37
Structure
x-ray diffraction · resolution 1.8 · 3 distinct chains · 25% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RING finger protein unkempt homolog | protein | 142 | 25% helix, 9% strand | Q8BL48 |
| B | RING finger protein unkempt homolog | protein | 140 | 24% helix, 9% strand | Q8BL48 |
| R | RNA (5'-R(*UP*UP*AP*UP*U)-3') | rna | 5 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.37 | 0.74 | 18 | empty |
| 2 | 60 | 0.31 | 0.76 | 15 | empty |
| 3 | 81 | 0.31 | 0.73 | 12 | empty |
| 4 | 53 | 0.28 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–R · 530 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 94 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ELH · Crystal structure of mouse unkempt zinc fingers 1-3 (ZNF1-3), bound to RNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q8BL48 · AlphaFold monomer V2.0 prediction for ring finger protein unkempt homolog (Q8BL48) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8BL48
- Elsewhere: RCSB PDB 5ELH · PDBe 5ELH · UniProt Q8BL48
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