MolNFT v1 · #88333 · protein
Crystal structure of 53BP1 tandem tudor domains in complex with methylated K810 rb peptide
4CRI · Tumor suppressor P53-binding protein 1: “Crystal structure of 53BP1 tandem tudor domains in complex with methylated K810 rb peptide”. X-ray diffraction, 3 pockets (best druggability 0.72). MolNFT v1 #88333 on GenesisL1: 3D…
- 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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