MolNFT v1 · #56706 · protein + DNA
Mouse NP95 sra domain DNA specific complex 2
2ZO1 · E3 ubiquitin-protein ligase UHRF1: “Mouse NP95 sra domain DNA specific complex 2”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #56706 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZO1
- Type
- protein + DNA
- Length
- 227 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; DNA (5'- D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP…
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Pockets
- 4 · best druggability 0.62
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 |
| D | DNA (5'- D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3') | dna | 9 | — | — |
| E | DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM) P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3') | dna | 12 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.62 | 0.87 | 20 | empty |
| 2 | 73 | 0.33 | 0.76 | 21 | empty |
| 3 | 64 | 0.31 | 0.75 | 12 | empty |
| 4 | 78 | 0.30 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–E · 912 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–D · 504 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–E · 411 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 2ZO1 · PDBe 2ZO1 · UniProt Q8VDF2
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