Research workbench
Structure and function of the RAD9-binding region of the DNA damage checkpoint adaptor TOPBP1
Analyse Structure and function of the RAD9-binding region of the DNA damage checkpoint… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XNK
- Type
- protein
- Length
- 1,160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-binding protein 1
- UniProt
- Q92547
- Pockets
- 16 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-binding protein 1 | protein | 291 | 37% helix, 14% strand | Q92547 |
| B, D | DNA topoisomerase 2-binding protein 1 | protein | 290 | 39% helix, 14% strand | Q92547 |
| C | DNA topoisomerase 2-binding protein 1 | protein | 289 | 38% helix, 16% strand | Q92547 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.61 | 0.78 | 34 | GOL |
| 2 | 249 | 0.61 | 0.80 | 31 | GOL |
| 3 | 253 | 0.56 | 0.77 | 32 | empty |
| 4 | 110 | 0.45 | 0.78 | 17 | empty |
| 5 | 114 | 0.44 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 933 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 901 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 2XNK · Structure and function of the Rad9-binding region of the DNA damage checkpoint adaptor… · the same entry in another collection · chain A against A, 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 0.98
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 2XNK · PDBe 2XNK · UniProt Q92547
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