MolNFT v1 · #63561 · protein + DNA
Mouse UHRF1 sra domain bound with hemi-methylated cpg DNA, crystal structure in space group C222(1) at 1.4 a resolution
3FDE · E3 ubiquitin-protein ligase UHRF1: “Mouse UHRF1 sra domain bound with hemi-methylated cpg DNA, crystal structure in space group C222(1) at 1.4 a…”. X-ray diffraction, 2 ligands (UNL, NA), 6 pockets (best druggability 0.70). MolNFT…
- PDB
- 3FDE
- Type
- protein + DNA
- Length
- 463 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'…
- EC
- 6.3.2.-
- UniProt
- Q8VDF2
- Ligands
- UNL, NA
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 209 | 17% helix, 27% strand | Q8VDF2 |
| B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 206 | 18% helix, 27% strand | Q8VDF2 |
| D, C | 5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3' | dna | 12 | — | — |
| E, F | 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 9 copies · chains A, B, D, C
- NA · Sodium ion · metal · 4 copies · chains A, D, E, B, C, F
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, E, C, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.70 | 0.77 | 63 | EDO |
| 2 | 108 | 0.70 | 0.93 | 17 | NA, EDO |
| 3 | 118 | 0.68 | 0.91 | 18 | NA, EDO |
| 4 | 383 | 0.63 | 0.78 | 50 | EDO |
| 5 | 99 | 0.41 | 0.78 | 23 | UNL |
Interfaces
9 interfaces between chains.
- A–D · 796 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 790 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–E · 572 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 545 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- C–F · 544 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3FDE · Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space… · the same entry in another collection · chain F against F, 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 B 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 3FDE · PDBe 3FDE · UniProt Q8VDF2
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