Research workbench
structure of UHRF2-SRA in complex with a 5mC-containing DNA
Analyse structure of UHRF2-SRA in complex with a 5mC-containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PW7
- Type
- protein + DNA
- Length
- 823 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.001
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- E3 ubiquitin-protein ligase UHRF2; 5mC-containing DNA1; 5mC-containing DNA2
- EC
- 6.3.2.-
- UniProt
- Q96PU4
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.001 · 6 distinct chains · 16% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 197 | 16% helix, 27% strand | Q96PU4 |
| B | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 189 | 16% helix, 29% strand | Q96PU4 |
| C, G | 5mC-containing DNA1 | dna | 12 | — | — |
| D, H | 5mC-containing DNA2 | dna | 12 | — | — |
| E | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 198 | 16% helix, 27% strand | Q96PU4 |
| F | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 191 | 16% helix, 28% strand | Q96PU4 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.69 | 0.82 | 48 | empty |
| 2 | 122 | 0.66 | 0.89 | 22 | empty |
| 3 | 134 | 0.66 | 0.89 | 26 | empty |
| 4 | 297 | 0.52 | 0.74 | 30 | empty |
| 5 | 247 | 0.47 | 0.73 | 23 | empty |
Interfaces
9 interfaces between chains.
- E–G · 761 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–C · 748 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–F · 649 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 467 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 465 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4PW7 · Structure of UHRF2-sra in complex with a 5MC-containing DNA · the same entry in another collection · chain H against H, TM-score 1.00
- Q96PU4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UHRF2 (Q96PU4) · a predicted model of the same protein · chain F 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 Q96PU4
- Elsewhere: RCSB PDB 4PW7 · PDBe 4PW7 · UniProt Q96PU4
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