Research workbench
Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide
Analyse Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RMM
- Type
- protein
- Length
- 790 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-binding protein 1; 53BP1
- UniProt
- Q92547
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 2-binding protein 1 | protein | 196 | 30% helix, 17% strand | Q92547 |
| C, D | DNA topoisomerase 2-binding protein 1 | protein | 190 | 35% helix, 16% strand | Q92547 |
| P, R | 53BP1 | protein | 9 | 0% helix, 22% strand | — |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.78 | 0.80 | 78 | empty |
| 2 | 409 | 0.72 | 0.83 | 39 | empty |
| 3 | 576 | 0.64 | 0.76 | 55 | empty |
| 4 | 189 | 0.49 | 0.76 | 31 | empty |
| 5 | 64 | 0.34 | 0.77 | 17 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1340 Ų buried · 9 hydrogen bonds · protein-protein
- D–P · 488 Ų buried · 7 hydrogen bonds · protein-protein
- C–R · 481 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 468 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 384 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6RMM · Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide · the same entry in another collection · chain R against R, TM-score 1.00
- Q92547 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-binding protein 1 (Q92547) · 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 Q92547
- Elsewhere: RCSB PDB 6RMM · PDBe 6RMM · UniProt Q92547
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