MolNFT v1 · #134392 · protein
Structure of the FHA1 domain of RAD53 bound simultaneously to the brct domain of DBF4 and a phosphopeptide.
5T2S · Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein…: “Structure of the FHA1 domain of RAD53 bound simultaneously to the brct domain of DBF4 and a phosphopeptide.”. X-ray diffraction, 4 pockets (best druggability 0.70).…
- PDB
- 5T2S
- Type
- protein
- Length
- 512 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…
- EC
- 2.7.12.1
- UniProt
- P32325, P22216
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 247 | 29% helix, 26% strand | P32325, P22216 |
| B, D | Asp-gly-glu-ser-tpo-asp-glu-asp-asp | protein | 9 | 0% helix, 0% strand | — |
| C | Ddk kinase regulatory subunit DBF4,SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 247 | 28% helix, 28% strand | P32325, P22216 |
Ligands and binding sites
- GOL · Glycerol · additive · 11 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.70 | 0.77 | 66 | GOL |
| 2 | 170 | 0.48 | 0.77 | 31 | empty |
| 3 | 105 | 0.42 | 0.77 | 25 | empty |
| 4 | 61 | 0.30 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2195 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 425 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 354 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5T2S · Structure of the FHA1 domain of Rad53 bound simultaneously to the BRCT domain of Dbf4 and… · the same entry in another collection · chain D against D, 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 0.52
- 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 0.52
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 5T2S · PDBe 5T2S · UniProt P32325 · UniProt P22216
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