Research workbench
Crystal structure of the brct domains of human 53BP1 bound to the P53 tumor supressor
Analyse Crystal structure of the brct domains of human 53BP1 bound to the P53 tumor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GZH
- Type
- protein
- Length
- 818 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, SO4
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 187 | 11% helix, 35% strand | P04637 |
| B | Tumor suppressor P53-binding protein 1 | protein | 224 | 32% helix, 18% strand | Q12888 |
| C | Cellular tumor antigen P53 | protein | 195 | 10% helix, 34% strand | P04637 |
| D | Tumor suppressor P53-binding protein 1 | protein | 212 | 32% helix, 19% strand | Q12888 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.63 | 0.75 | 44 | empty |
| 2 | 155 | 0.45 | 0.76 | 31 | empty |
| 3 | 161 | 0.41 | 0.74 | 31 | empty |
| 4 | 94 | 0.38 | 0.76 | 19 | empty |
| 5 | 108 | 0.36 | 0.74 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 650 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 593 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 247 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 182 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1GZH · Crystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor · 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 0.99
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 1GZH · PDBe 1GZH · UniProt P04637 · UniProt Q12888
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