MolNFT v1 · #103953 · protein + DNA
Structure of UHRF2-sra in complex with a 5HMC-containing DNA, complex II
4PW6 · E3 ubiquitin-protein ligase UHRF2: “Structure of UHRF2-sra in complex with a 5HMC-containing DNA, complex II”. X-ray diffraction, 7 pockets (best druggability 0.69). MolNFT v1 #103953 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PW6
- Type
- protein + DNA
- Length
- 400 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF2; 5HMC-containing DNA1; 5HMC-containing DNA2
- EC
- 6.3.2.-
- UniProt
- Q96PU4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 188 | 16% helix, 28% strand | Q96PU4 |
| C | 5HMC-containing DNA1 | dna | 12 | — | — |
| D | 5HMC-containing DNA2 | dna | 12 | — | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.69 | 0.81 | 36 | empty |
| 2 | 66 | 0.58 | 0.90 | 18 | empty |
| 3 | 54 | 0.52 | 0.88 | 17 | empty |
| 4 | 214 | 0.43 | 0.73 | 24 | empty |
| 5 | 136 | 0.35 | 0.72 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–D · 618 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–C · 590 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 498 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–D · 372 Ų buried · 4 hydrogen bonds · protein-nucleic
- B–C · 370 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4PW6 · structure of UHRF2-SRA in complex with a 5hmC-containing DNA, complex II · the same entry in another collection · chain A against A, 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 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 Q96PU4
- Elsewhere: RCSB PDB 4PW6 · PDBe 4PW6 · UniProt Q96PU4
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