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Bifunctional histidine kinase CckA (domain, CA) in complex with c-di-GMP and AMPPNP/Mg2+
Analyse Bifunctional histidine kinase CckA (domain, CA) in complex with c-di-GMP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IDM
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Caulobacter vibrioides
- Molecule
- Cell cycle histidine kinase CckA
- UniProt
- Q9X688
- Ligands
- ANP, C2E, MG
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell cycle histidine kinase CckA | protein | 177 | 33% helix, 28% strand | Q9X688 |
| B | Cell cycle histidine kinase CckA | protein | 177 | 33% helix, 29% strand | Q9X688 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.68 | 0.83 | 36 | ANP, MG |
| 2 | 300 | 0.67 | 0.82 | 30 | ANP, MG |
| 3 | 196 | 0.49 | 0.76 | 22 | empty |
| 4 | 112 | 0.37 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1006 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5IDM · Bifunctional histidine kinase ccka (domain, ca) in complex with C-di- gmp and AMPPNP/MG2+ · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9X688
- Elsewhere: RCSB PDB 5IDM · PDBe 5IDM · UniProt Q9X688
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