Research workbench
Crystal structure of the sra domain of mouse NP95 in complex with hemi-methylated cpg DNA
Analyse Crystal structure of the sra domain of mouse NP95 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZKE
- Type
- protein + DNA
- Length
- 234 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*…
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 210 | 17% helix, 27% strand | Q8VDF2 |
| C | DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)- 3') | dna | 12 | — | — |
| D | DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM) P*DGP*DGP*DTP*DAP*DG)-3') | dna | 12 | — | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.68 | 0.91 | 19 | empty |
| 2 | 173 | 0.42 | 0.74 | 17 | empty |
| 3 | 51 | 0.38 | 0.81 | 13 | empty |
| 4 | 87 | 0.37 | 0.76 | 21 | empty |
| 5 | 65 | 0.31 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–D · 916 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 772 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–D · 530 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2ZKE · 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 2ZKE · PDBe 2ZKE · UniProt Q8VDF2
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