Research workbench
Crystal structure of 53BP1 tandem tudor domains in complex with methylated K810 rb peptide
Analyse Crystal structure of 53BP1 tandem tudor domains in complex with methylated K810… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CRI
- Type
- protein
- Length
- 251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor suppressor P53-binding protein 1; RB1 protein
- UniProt
- Q12888, P78495
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tumor suppressor P53-binding protein 1 | protein | 119 | 13% helix, 53% strand | Q12888 |
| C | RB1 protein | protein | 7 | 0% helix, 14% strand | P78495 |
| D | RB1 protein | protein | 6 | 0% helix, 0% strand | P78495 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.72 | 0.96 | 24 | empty |
| 2 | 109 | 0.49 | 0.80 | 18 | empty |
| 3 | 71 | 0.43 | 0.81 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–B · 566 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 545 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 418 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 74 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 53 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified, 1 disulfide (methylation, disulfide).
Compared structures
- 4CRI · Crystal Structure of 53BP1 tandem tudor domains in complex with methylated K810 Rb peptide · 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 A against A, TM-score 0.97
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
- Every structure of UniProt P78495
- Elsewhere: RCSB PDB 4CRI · PDBe 4CRI · UniProt Q12888 · UniProt P78495
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