Research workbench
Crystal structure of TOPBP1 BRCT4/5 in complex with a blm phosphopeptide
Analyse Crystal structure of TOPBP1 BRCT4/5 in complex with a blm phosphopeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U6K
- Type
- protein
- Length
- 1,551 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-binding protein 1; Bloom sydrome recq helicase like protein (blm)
- UniProt
- Q6ZQF0
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA topoisomerase 2-binding protein 1 | protein | 190 | 35% helix, 15% strand | Q6ZQF0 |
| E, F, G, H | DNA topoisomerase 2-binding protein 1 | protein | 191 | 32% helix, 16% strand | Q6ZQF0 |
| L, M | Bloom sydrome recq helicase like protein (blm) | protein | 6 | 0% helix, 17% strand | — |
| N | Bloom sydrome recq helicase like protein (blm) | protein | 5 | 0% helix, 20% strand | — |
| O | Bloom sydrome recq helicase like protein (blm) | protein | 10 | 0% helix, 20% strand | — |
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.76 | 0.78 | 79 | empty |
| 2 | 1014 | 0.76 | 0.78 | 68 | empty |
| 3 | 191 | 0.51 | 0.77 | 22 | empty |
| 4 | 192 | 0.50 | 0.76 | 21 | empty |
| 5 | 127 | 0.50 | 0.80 | 24 | empty |
Interfaces
15 interfaces between chains.
- C–G · 590 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 571 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 561 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 548 Ų buried · 9 hydrogen bonds · protein-protein
- D–O · 448 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5U6K · Crystal structure of TopBP1 BRCT4/5 in complex with a BLM phosphopeptide · the same entry in another collection · chain O against O, TM-score 1.00
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 Q6ZQF0
- Elsewhere: RCSB PDB 5U6K · PDBe 5U6K · UniProt Q6ZQF0
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