MolNFT v1 · #56608 · protein + DNA
Crystal structure of the sra domain of mouse NP95 in complex with hemi-methylated cpg DNA
2ZKD · DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)…: “Crystal structure of the sra domain of mouse NP95 in complex with hemi-methylated cpg DNA”. X-ray diffraction, 8 pockets (best druggability 0.67). MolNFT v1 #56608 on…
- PDB
- 2ZKD
- Type
- protein + DNA
- Length
- 467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)- 3'); DNA…
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)- 3') | dna | 12 | — | — |
| D, F | DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM) P*DGP*DGP*DTP*DAP*DG)-3') | dna | 12 | — | — |
| A | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 210 | 15% helix, 27% strand | Q8VDF2 |
| B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 209 | 15% helix, 27% strand | Q8VDF2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.67 | 0.94 | 18 | empty |
| 2 | 598 | 0.65 | 0.76 | 42 | empty |
| 3 | 213 | 0.63 | 0.83 | 35 | empty |
| 4 | 570 | 0.61 | 0.74 | 53 | empty |
| 5 | 68 | 0.43 | 0.81 | 18 | empty |
Interfaces
11 interfaces between chains.
- D–A · 921 Ų buried · 17 hydrogen bonds · protein-nucleic
- F–B · 903 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–B · 777 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 762 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–D · 535 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2ZKD · Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA · 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 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 Q8VDF2
- Elsewhere: RCSB PDB 2ZKD · PDBe 2ZKD · UniProt Q8VDF2
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