MolNFT v1 · #88598 · protein
Crystal structure of the kinase domain of CIPK23
4CZT · Cbl-interacting SERINE/THREONINE-protein kinase 23: “Crystal structure of the kinase domain of CIPK23”. X-ray diffraction, 2 ligands (CPS, SO4), 17 pockets (best druggability 0.87). MolNFT v1 #88598 on GenesisL1: 3D structure…
- PDB
- 4CZT
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cbl-interacting SERINE/THREONINE-protein kinase 23
- EC
- 2.7.11.1
- UniProt
- Q93VD3
- Ligands
- CPS, SO4
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cbl-interacting SERINE/THREONINE-protein kinase 23 (EC 2.7.11.1) | protein | 294 | 37% helix, 16% strand | Q93VD3 |
| B | Cbl-interacting SERINE/THREONINE-protein kinase 23 (EC 2.7.11.1) | protein | 286 | 38% helix, 17% strand | Q93VD3 |
| C | Cbl-interacting SERINE/THREONINE-protein kinase 23 (EC 2.7.11.1) | protein | 286 | 40% helix, 16% strand | Q93VD3 |
| D | Cbl-interacting SERINE/THREONINE-protein kinase 23 (EC 2.7.11.1) | protein | 302 | 37% helix, 16% strand | Q93VD3 |
Ligands and binding sites
- CPS · 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate · ligand · 7 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 21 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.87 | 0.88 | 92 | CPS |
| 2 | 550 | 0.79 | 0.86 | 52 | CPS |
| 3 | 926 | 0.78 | 0.81 | 81 | SO4 |
| 4 | 353 | 0.75 | 0.85 | 35 | CPS |
| 5 | 92 | 0.73 | 0.96 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1701 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1656 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 995 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4CZT · Crystal structure of the kinase domain of CIPK23 · the same entry in another collection · chain D against D, TM-score 1.00
- Q93VD3 · AlphaFold monomer V2.0 prediction for cbl-interacting SERINE/THREONINE-protein kinase 23… · a predicted model of the same protein · chain C against A, TM-score 0.89
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 Q93VD3
- Elsewhere: RCSB PDB 4CZT · PDBe 4CZT · UniProt Q93VD3
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