Research workbench
Structure of 53BP1 tudor domains in complex with small molecule UNC3474
Analyse Structure of 53BP1 tudor domains in complex with small molecule UNC3474 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MXZ
- Type
- protein
- Length
- 1,195 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TP53-binding protein 1
- UniProt
- Q12888
- Ligands
- K6S
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 14% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | TP53-binding protein 1 | protein | 119 | 14% helix, 51% strand | Q12888 |
| B, D, I | TP53-binding protein 1 | protein | 120 | 14% helix, 50% strand | Q12888 |
| C, H | TP53-binding protein 1 | protein | 119 | 14% helix, 52% strand | Q12888 |
| E | TP53-binding protein 1 | protein | 120 | 14% helix, 53% strand | Q12888 |
| G | TP53-binding protein 1 | protein | 121 | 14% helix, 51% strand | Q12888 |
| J | TP53-binding protein 1 | protein | 118 | 14% helix, 53% strand | Q12888 |
Ligands and binding sites
- K6S · N-[3-(tert-butylamino)propyl]-3-(propan-2-yl)benzamide · ligand · 5 copies · chains A, B, C, D, E, F, G, H, I, J
- FMT · Formic acid · additive · 7 copies · chains B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.82 | 0.98 | 22 | K6S |
| 2 | 131 | 0.80 | 0.97 | 20 | K6S |
| 3 | 129 | 0.80 | 0.97 | 20 | K6S |
| 4 | 126 | 0.80 | 0.97 | 21 | K6S |
| 5 | 121 | 0.79 | 0.96 | 21 | K6S |
Interfaces
15 interfaces between chains.
- E–F · 1084 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1075 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1044 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1042 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1039 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6MXZ · Structure of 53BP1 Tudor domains in complex with small molecule UNC3474 · the same entry in another collection · chain J against J, TM-score 1.00
- Q12888 · AlphaFold monomer V2.0 prediction for TP53-binding protein 1 (Q12888) · a predicted model of the same protein · chain J 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 6MXZ · PDBe 6MXZ · UniProt Q12888
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