MolNFT v1 · #157403 · protein
Structure of 53BP1 tandem tudor domains in complex with small molecule UNC3351
6MXY · TP53-binding protein 1: “Structure of 53BP1 tandem tudor domains in complex with small molecule UNC3351”. X-ray diffraction, 2 ligands (K6M, PO4), 2 pockets (best druggability 0.78). MolNFT v1 #157403 on GenesisL1: 3D structure…
- PDB
- 6MXY
- Type
- protein
- Length
- 245 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TP53-binding protein 1
- UniProt
- Q12888
- Ligands
- K6M, PO4
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TP53-binding protein 1 | protein | 123 | 14% helix, 50% strand | Q12888 |
| B | TP53-binding protein 1 | protein | 122 | 12% helix, 51% strand | Q12888 |
Ligands and binding sites
- K6M · N-[3-(tert-butylamino)propyl]-3-(trifluoromethyl) benzamide · ligand · chains A, B
- PO4 · Phosphate ion · ion · 5 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 | 117 | 0.78 | 0.96 | 20 | K6M |
| 2 | 178 | 0.57 | 0.81 | 29 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1084 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6MXY · Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC3351 · 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 B against A, TM-score 0.93
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 6MXY · PDBe 6MXY · UniProt Q12888
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