Research workbench
Crystal structure of a helicobacter pylori proinflammatory kinase ctka
Analyse Crystal structure of a helicobacter pylori proinflammatory kinase ctka in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AKK
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ctka
- EC
- 2.7.11.1
- UniProt
- Q9ZKJ5
- Ligands
- ADP, MG
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ctka (EC 2.7.11.1) | protein | 296 | 43% helix, 17% strand | Q9ZKJ5 |
| B | Ctka (EC 2.7.11.1) | protein | 288 | 46% helix, 16% strand | Q9ZKJ5 |
| C | Ctka (EC 2.7.11.1) | protein | 285 | 44% helix, 16% strand | Q9ZKJ5 |
| D | Ctka (EC 2.7.11.1) | protein | 288 | 44% helix, 16% strand | Q9ZKJ5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.84 | 0.86 | 116 | ADP |
| 2 | 990 | 0.84 | 0.85 | 103 | ADP, MG |
| 3 | 370 | 0.73 | 0.84 | 52 | empty |
| 4 | 373 | 0.64 | 0.79 | 51 | empty |
| 5 | 159 | 0.63 | 0.85 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1593 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1580 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 642 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 539 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3AKK · Crystal structure of A Helicobacter pylori proinflammatory kinase CtkA · the same entry in another collection · chain B against B, TM-score 1.00
- Q9ZKJ5 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase ctka (Q9ZKJ5) · 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 Q9ZKJ5
- Elsewhere: RCSB PDB 3AKK · PDBe 3AKK · UniProt Q9ZKJ5
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