MolNFT v1 · #103338 · protein
Crystal structure of RAD53 kinase domain and SCD2
4PDP · SERINE/THREONINE-protein kinase RAD53: “Crystal structure of RAD53 kinase domain and SCD2”. X-ray diffraction, 6 pockets (best druggability 0.68). MolNFT v1 #103338 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PDP
- Type
- protein
- Length
- 526 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
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 261 | 42% helix, 17% strand | P22216 |
| B | SERINE/THREONINE-protein kinase RAD53 (EC 2.7.12.1) | protein | 265 | 40% helix, 17% strand | P22216 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.68 | 0.84 | 29 | empty |
| 2 | 290 | 0.58 | 0.77 | 37 | empty |
| 3 | 128 | 0.42 | 0.75 | 19 | empty |
| 4 | 65 | 0.35 | 0.77 | 12 | empty |
| 5 | 61 | 0.33 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 785 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 4PDP · PDBe 4PDP · UniProt P22216
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