MolNFT v1 · #63398 · protein + DNA
Mouse UHRF1 sra domain bound with hemi-methylated cpg, crystal structure in space group P21
3F8I · E3 ubiquitin-protein ligase UHRF1: “Mouse UHRF1 sra domain bound with hemi-methylated cpg, crystal structure in space group P21”. X-ray diffraction, 7 pockets (best druggability 0.67). MolNFT v1 #63398 on GenesisL1: 3D structure…
- PDB
- 3F8I
- Type
- protein + DNA
- Length
- 460 residues
- Chains
- 6
- 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)…
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 206 | 17% helix, 28% strand | Q8VDF2 |
| D, F | 5'-D(*DCP*DCP*DAP*DTP*DGP*(5CM) P*DGP*DCP*DTP*DGP*DAP*DC)-3' | dna | 12 | — | — |
| E, G | 5'- D(*DGP*DTP*DCP*DAP*DGP*DCP*DGP*DCP*DAP*DTP*DGP*DG)-3' | dna | 12 | — | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.67 | 0.88 | 18 | empty |
| 2 | 124 | 0.66 | 0.90 | 18 | empty |
| 3 | 229 | 0.47 | 0.74 | 27 | empty |
| 4 | 196 | 0.45 | 0.74 | 25 | empty |
| 5 | 56 | 0.41 | 0.82 | 15 | empty |
Interfaces
10 interfaces between chains.
- B–F · 781 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–D · 772 Ų buried · 14 hydrogen bonds · protein-nucleic
- F–G · 547 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- D–E · 534 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–E · 488 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3F8I · Mouse UHRF1 SRA domain bound with hemi-methylated CpG, crystal structure in space group… · the same entry in another collection · chain D against D, 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 A 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 3F8I · PDBe 3F8I · UniProt Q8VDF2
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