Research workbench
Structure of the FHA1 domain of RAD53 bound to the brct domain of DBF4
Analyse Structure of the FHA1 domain of RAD53 bound to the brct domain of DBF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T2F
- Type
- protein
- Length
- 973 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein kinase RAD53 chimeric protein
- EC
- 2.7.12.1
- UniProt
- P32325, P22216
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein kinase RAD53 chimeric protein (EC 2.7.12.1) | protein | 237 | 29% helix, 29% strand | P32325, P22216 |
| B | Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein kinase RAD53 chimeric protein (EC 2.7.12.1) | protein | 244 | 30% helix, 25% strand | P32325, P22216 |
| C | Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein kinase RAD53 chimeric protein (EC 2.7.12.1) | protein | 248 | 30% helix, 28% strand | P32325, P22216 |
| D | Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein kinase RAD53 chimeric protein (EC 2.7.12.1) | protein | 244 | 30% helix, 27% strand | P32325, P22216 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.68 | 0.77 | 54 | EDO |
| 2 | 543 | 0.67 | 0.77 | 50 | EDO |
| 3 | 161 | 0.49 | 0.77 | 29 | empty |
| 4 | 150 | 0.45 | 0.76 | 27 | empty |
| 5 | 82 | 0.40 | 0.78 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2184 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2154 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 120 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 57 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5T2F · Structure of the FHA1 domain of Rad53 bound to the BRCT domain of Dbf4 · the same entry in another collection · chain B against B, TM-score 1.00
- P22216 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase RAD53 (P22216) · a predicted model of the same protein · chain A against A, TM-score 0.53
- P32325 · AlphaFold monomer V2.0 prediction for ddk kinase regulatory subunit DBF4 (P32325) · a predicted model of the same protein · chain C against A, TM-score 0.53
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 P32325
- Every structure of UniProt P22216
- Elsewhere: RCSB PDB 5T2F · PDBe 5T2F · UniProt P32325 · UniProt P22216
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.