MolNFT v1 · #103952 · protein + DNA
Structure of UHRF2-sra in complex with a 5HMC-containing DNA, complex I
4PW5 · E3 ubiquitin-protein ligase UHRF2: “Structure of UHRF2-sra in complex with a 5HMC-containing DNA, complex I”. X-ray diffraction, 14 pockets (best druggability 0.68). MolNFT v1 #103952 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4PW5
- Type
- protein + DNA
- Length
- 798 residues
- Chains
- 8
- 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
- 14 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 189 | 16% helix, 29% strand | Q96PU4 |
| B | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 188 | 16% helix, 28% strand | Q96PU4 |
| C, G | 5HMC-containing DNA1 | dna | 12 | — | — |
| D, H | 5HMC-containing DNA2 | dna | 11 | — | — |
| E | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 188 | 16% helix, 29% strand | Q96PU4 |
| F | E3 ubiquitin-protein ligase UHRF2 (EC 6.3.2.-) | protein | 187 | 17% helix, 28% strand | Q96PU4 |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.68 | 0.92 | 21 | empty |
| 2 | 111 | 0.67 | 0.91 | 22 | empty |
| 3 | 340 | 0.67 | 0.81 | 49 | empty |
| 4 | 85 | 0.35 | 0.75 | 12 | empty |
| 5 | 84 | 0.32 | 0.74 | 11 | empty |
Interfaces
9 interfaces between chains.
- A–F · 639 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 611 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–G · 603 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–D · 492 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- G–H · 483 Ų buried · 52 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4PW5 · structure of UHRF2-SRA in complex with a 5hmC-containing DNA, complex I · 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 4PW5 · PDBe 4PW5 · UniProt Q96PU4
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