Research workbench
Structure of UHRF1 phd finger in complex with histone H3K4ME3 1-9 peptide
Analyse Structure of UHRF1 phd finger in complex with histone H3K4ME3 1-9 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SOW
- Type
- protein
- Length
- 144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; Histone H3
- EC
- 6.3.2.-
- UniProt
- Q96T88
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 67 | 9% helix, 10% strand | Q96T88 |
| B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 65 | 5% helix, 11% strand | Q96T88 |
| C, D | Histone H3 | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.48 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 458 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 445 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 359 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 3SOW · Structure of UHRF1 PHD finger in complex with histone H3K4me3 1-9 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q96T88 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase UHRF1 (Q96T88) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q96T88
- Elsewhere: RCSB PDB 3SOW · PDBe 3SOW · UniProt Q96T88
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