Research workbench
Tudor domain of tumor suppressor P53BP1 with small molecule ligand
Analyse Tudor domain of tumor suppressor P53BP1 with small molecule ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RG2
- Type
- protein
- Length
- 240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor suppressor P53-binding protein 1
- UniProt
- Q12888
- Ligands
- 3OO, UNX
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor suppressor P53-binding protein 1 | protein | 119 | 14% helix, 51% strand | Q12888 |
| B | Tumor suppressor P53-binding protein 1 | protein | 121 | 12% helix, 54% strand | Q12888 |
Ligands and binding sites
- 3OO · 3-bromo-N-[3-(tert-butylamino)propyl]benzamide · ligand · chains A, B
- UNX · Unknown atom or ion · ion · 12 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.98 | 23 | 3OO, UNX |
| 2 | 170 | 0.64 | 0.85 | 35 | UNX |
Interfaces
1 interface between chains.
- A–B · 1056 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4RG2 · Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand · the same entry in another collection · chain A against A, TM-score 1.00
- Q12888 · AlphaFold monomer V2.0 prediction for TP53-binding protein 1 (Q12888) · 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 Q12888
- Elsewhere: RCSB PDB 4RG2 · PDBe 4RG2 · UniProt Q12888
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