MolNFT v1 · #11770 · protein
Crystal structure of human protein kinase CK2 holoenzyme
1JWH · Casein kinase II, alpha chain: “Crystal structure of human protein kinase CK2 holoenzyme”. X-ray diffraction, 3 ligands (ANP, ZN, PO4), 13 pockets (best druggability 0.75). MolNFT v1 #11770 on GenesisL1: 3D structure, binding sites…
- PDB
- 1JWH
- Type
- protein
- Length
- 1,075 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II, alpha chain; Casein kinase II beta chain
- EC
- 2.7.1.37
- UniProt
- P68400, P67870
- Ligands
- ANP, ZN, PO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II, alpha chain (EC 2.7.1.37) | protein | 336 | 37% helix, 12% strand | P68400 |
| B | Casein kinase II, alpha chain (EC 2.7.1.37) | protein | 335 | 33% helix, 12% strand | P68400 |
| C | Casein kinase II beta chain | protein | 200 | 38% helix, 7% strand | P67870 |
| D | Casein kinase II beta chain | protein | 204 | 37% helix, 6% strand | P67870 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains C, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.75 | 0.79 | 74 | empty |
| 2 | 574 | 0.75 | 0.82 | 55 | empty |
| 3 | 52 | 0.71 | 0.98 | 20 | empty |
| 4 | 510 | 0.68 | 0.78 | 50 | empty |
| 5 | 307 | 0.63 | 0.79 | 38 | ANP |
Interfaces
5 interfaces between chains.
- C–D · 1822 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 535 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 520 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 468 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1JWH · Crystal Structure of Human Protein Kinase CK2 Holoenzyme · the same entry in another collection · chain D against D, TM-score 1.00
- P68400 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P68400) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P67870 · AlphaFold monomer V2.0 prediction for casein kinase II subunit beta (P67870) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P68400
- Every structure of UniProt P67870
- Elsewhere: RCSB PDB 1JWH · PDBe 1JWH · UniProt P68400 · UniProt P67870
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