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
- 3AKL
- Type
- protein
- Length
- 1,120 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
- ANP, ADP, MG
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ctka (EC 2.7.11.1) | protein | 281 | 43% helix, 17% strand | Q9ZKJ5 |
| C, D | Ctka (EC 2.7.11.1) | protein | 279 | 43% helix, 18% strand | Q9ZKJ5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains A, B, D
- ADP · Adenosine-5'-diphosphate · ligand · chains C
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.82 | 0.83 | 91 | ANP, MG |
| 2 | 1024 | 0.82 | 0.83 | 93 | ADP, MG, ANP |
| 3 | 464 | 0.60 | 0.75 | 44 | empty |
| 4 | 154 | 0.49 | 0.78 | 29 | empty |
| 5 | 195 | 0.48 | 0.75 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1409 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1404 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 521 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 104 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3AKL · Crystal structure of A Helicobacter pylori proinflammatory kinase CtkA · the same entry in another collection · chain D against D, 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 B 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 3AKL · PDBe 3AKL · UniProt Q9ZKJ5
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