MolNFT v1 · #104957 · protein
Crystal structure of tandem tudor domains of UHRF1 in complex with a small organic molecule
4QQD · E3 ubiquitin-protein ligase UHRF1: “Crystal structure of tandem tudor domains of UHRF1 in complex with a small organic molecule”. X-ray diffraction, 2 ligands (36X, UNX), 1 pocket (best druggability 0.68). MolNFT v1 #104957 on…
- PDB
- 4QQD
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase UHRF1
- EC
- 6.3.2.-
- UniProt
- Q96T88
- Ligands
- 36X, UNX
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 134 | 7% helix, 50% strand | Q96T88 |
| B | E3 ubiquitin-protein ligase UHRF1 (EC 6.3.2.-) | protein | 136 | 9% helix, 48% strand | Q96T88 |
Ligands and binding sites
- 36X · 4-methyl-2,3,4,5,6,7-hexahydrodicyclopenta[b,e]pyridin-8(1H)-imine · ligand · 3 copies · chains A, B
- UNX · Unknown atom or ion · ion · 5 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.68 | 0.83 | 33 | UNX, 36X |
Interfaces
1 interface between chains.
- A–B · 548 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4QQD · Crystal Structure of tandem tudor domains of UHRF1 in complex with a small organic… · 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 0.96
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 4QQD · PDBe 4QQD · UniProt Q96T88
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