MolNFT v1 · #134380 · protein
Structure of the FHA1 domain of RAD53 bound to the brct domain of DBF4
5T2F · Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein…: “Structure of the FHA1 domain of RAD53 bound to the brct domain of DBF4”. X-ray diffraction, 10 pockets (best druggability 0.68). MolNFT v1 #134380 on GenesisL1: 3D…
- 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
- 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
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