Research workbench
Phd finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail
Analyse Phd finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZVY
- Type
- protein
- Length
- 141 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1; Histone H3.1
- EC
- 6.3.2.-
- UniProt
- Q96T88, P68431
- Ligands
- ZN, CL
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 65 | 9% helix, 12% strand | Q96T88 |
| B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 66 | 5% helix, 12% strand | Q96T88 |
| C, D | Histone H3.1 | protein | 5 | 0% helix, 20% strand | P68431 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 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 | 65 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 484 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 366 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3ZVY · PHD finger of human UHRF1 in complex with unmodified histone H3 N- terminal tail · 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 A 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
- Every structure of UniProt P68431
- Elsewhere: RCSB PDB 3ZVY · PDBe 3ZVY · UniProt Q96T88 · UniProt P68431
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