MolNFT v1 · #81033 · protein
Crystal structure of TOPBP1 BRCT4/5 domains in complex with a phospho- peptide
3UEO · DNA topoisomerase 2-binding protein 1: “Crystal structure of TOPBP1 BRCT4/5 domains in complex with a phospho- peptide”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #81033 on GenesisL1: 3D structure, binding…
- PDB
- 3UEO
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-binding protein 1; Phospho-peptide
- UniProt
- Q92547
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 2-binding protein 1 | protein | 186 | 35% helix, 17% strand | Q92547 |
| C, D | DNA topoisomerase 2-binding protein 1 | protein | 186 | 34% helix, 19% strand | Q92547 |
| E | Phospho-peptide | protein | 10 | 0% helix, 20% strand | — |
| F | Phospho-peptide | protein | 8 | 0% helix, 25% strand | — |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.79 | 0.83 | 61 | empty |
| 2 | 75 | 0.70 | 0.95 | 20 | empty |
| 3 | 167 | 0.57 | 0.82 | 29 | empty |
| 4 | 199 | 0.51 | 0.77 | 24 | empty |
| 5 | 101 | 0.51 | 0.82 | 22 | empty |
Interfaces
10 interfaces between chains.
- C–D · 707 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 698 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 631 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 507 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 311 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3UEO · Crystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide · the same entry in another collection · chain D against D, 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 A 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 Q92547
- Elsewhere: RCSB PDB 3UEO · PDBe 3UEO · UniProt Q92547
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