MolNFT v1 · #56610 · protein + DNA
Crystal structure of the sra domain of mouse NP95 in complex with hemi-methylated cpg DNA
2ZKF · E3 ubiquitin-protein ligase UHRF1: “Crystal structure of the sra domain of mouse NP95 in complex with hemi-methylated cpg DNA”. X-ray diffraction, 2 pockets (best druggability 0.65). MolNFT v1 #56610 on GenesisL1: 3D structure…
- PDB
- 2ZKF
- Type
- protein + DNA
- Length
- 231 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)…
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 209 | 15% helix, 27% strand | Q8VDF2 |
| C | DNA (5'-D(P*DCP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DAP*DGP*DA)- 3') | dna | 11 | — | — |
| D | DNA (5'-D(*DCP*DTP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DGP*DA)- 3') | dna | 11 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.65 | 0.84 | 33 | empty |
| 2 | 58 | 0.42 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–D · 912 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 741 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 466 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2ZKF · Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA · the same entry in another collection · chain A against A, 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 2ZKF · PDBe 2ZKF · UniProt Q8VDF2
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