Research workbench
Structure of human protein kinase CK2 catalytic subunit in complex with a CK2BETA-competitive cyclic peptide
Analyse Structure of human protein kinase CK2 catalytic subunit in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IB5
- Type
- protein
- Length
- 1,044 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Casein kinase II subunit alpha; CK2BETA-derived cyclic peptide
- EC
- 2.7.11.1
- UniProt
- P68400
- Ligands
- CL
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 331 | 42% helix, 15% strand | P68400 |
| B | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 329 | 40% helix, 13% strand | P68400 |
| C | Casein kinase II subunit alpha (EC 2.7.11.1) | protein | 332 | 40% helix, 15% strand | P68400 |
| D, E, F, G | CK2BETA-derived cyclic peptide | protein | 13 | 0% helix, 38% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, C
- GOL · Glycerol · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.79 | 0.81 | 112 | GOL, CL |
| 2 | 685 | 0.71 | 0.78 | 57 | empty |
| 3 | 407 | 0.70 | 0.81 | 48 | GOL |
| 4 | 405 | 0.66 | 0.79 | 51 | GOL |
| 5 | 92 | 0.38 | 0.76 | 21 | empty |
Interfaces
7 interfaces between chains.
- C–F · 555 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 547 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 529 Ų buried · 3 hydrogen bonds · protein-protein
- C–G · 408 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 330 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4IB5 · Structure of human protein kinase CK2 catalytic subunit in complex with a… · the same entry in another collection · chain G against G, 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 C against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 4IB5 · PDBe 4IB5 · UniProt P68400
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