MolNFT v1 · #103341 · protein
Crystal structure of RAD53 kinase domain and SCD2 in complex with amppnp
4PDS · SERINE/THREONINE-protein kinase RAD53: “Crystal structure of RAD53 kinase domain and SCD2 in complex with amppnp”. X-ray diffraction, 1 ligand (ANP), 3 pockets (best druggability 0.73). MolNFT v1 #103341 on GenesisL1: 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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