Research workbench
Crystal structure of RAD53 kinase domain and SCD2 in complex with amppnp
Analyse Crystal structure of RAD53 kinase domain and SCD2 in complex with amppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PDS
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase RAD53
- EC
- 2.7.12.1
- UniProt
- P22216
- Ligands
- ANP
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 249 | 41% helix, 16% strand | P22216 |
| B | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 248 | 42% helix, 15% strand | P22216 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.73 | 0.83 | 55 | empty |
| 2 | 193 | 0.50 | 0.76 | 29 | ANP |
| 3 | 129 | 0.44 | 0.76 | 25 | ANP |
Interfaces
1 interface between chains.
- A–B · 655 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4PDS · Crystal structure of Rad53 kinase domain and SCD2 in complex with AMPPNP · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.97
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 P22216
- Elsewhere: RCSB PDB 4PDS · PDBe 4PDS · UniProt P22216
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