Research workbench
Crystal structure of the 53BP1 brct region complexed to tumor suppressor P53
Analyse Crystal structure of the 53BP1 brct region complexed to tumor suppressor P53 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KZY
- Type
- protein
- Length
- 854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; Tumor suppressor P53-binding protein 1
- UniProt
- P04637, Q12888
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellular tumor antigen P53 | protein | 195 | 7% helix, 34% strand | P04637 |
| C, D | Tumor suppressor P53-binding protein 1 | protein | 232 | 32% helix, 18% strand | Q12888 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.76 | 0.78 | 109 | empty |
| 2 | 169 | 0.46 | 0.76 | 27 | empty |
| 3 | 79 | 0.37 | 0.77 | 17 | empty |
| 4 | 71 | 0.37 | 0.77 | 21 | empty |
| 5 | 77 | 0.33 | 0.75 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 639 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 626 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 447 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 149 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1KZY · Crystal Structure of the 53bp1 BRCT Region Complexed to Tumor Suppressor P53 · 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 C against A, TM-score 0.98
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 P04637
- Every structure of UniProt Q12888
- Elsewhere: RCSB PDB 1KZY · PDBe 1KZY · UniProt P04637 · UniProt Q12888
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