MolNFT v1 · #13058 · protein
Crystal structure of the 53BP1 brct region complexed to tumor suppressor P53
1KZY · Cellular tumor antigen P53: “Crystal structure of the 53BP1 brct region complexed to tumor suppressor P53”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.76). MolNFT v1 #13058 on GenesisL1: 3D structure, binding…
- 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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