Research workbench
Mouse UHRF1 sra domain bound with hemi-methylated cpg, crystal structure in space group C222(1)
Analyse Mouse UHRF1 sra domain bound with hemi-methylated cpg, crystal structure in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F8J
- Type
- protein + DNA
- Length
- 230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC…
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 206 | 19% helix, 28% strand | Q8VDF2 |
| F | 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM)P*DGP*DCP*DTP*DGP*DAP*DC)- 3' | dna | 12 | — | — |
| G | 5'-D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3' | dna | 12 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.63 | 0.88 | 18 | empty |
| 2 | 353 | 0.57 | 0.76 | 39 | GOL |
| 3 | 75 | 0.36 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–F · 790 Ų buried · 13 hydrogen bonds · protein-nucleic
- F–G · 539 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- B–G · 536 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3F8J · Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8VDF2 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UHRF1 (Q8VDF2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8VDF2
- Elsewhere: RCSB PDB 3F8J · PDBe 3F8J · UniProt Q8VDF2
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