5YVB: CaMKK2

Structure of CaMKK2 in complex with CKI-011. Determined by X-ray diffraction at 2.02 Å resolution. Released 5 Dec 2018.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,359
Mol. weight: 34.53 kDa
Ligands: 92C
Released: 5 Dec 2018

Explore 5YVB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YVB contains 13 α-helices and 14 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	161-162	2	1
β-strand	165-173	9	1
β-strand	178-184	7	1
β-strand	189-197	9	1
α-helix	230-241	12
β-strand	248	1	2
β-strand	251-256	6	1
β-strand	262-268	7	1
β-strand	274	1	2
α-helix	283-285	3
α-helix	286-305	20
β-strand	308-309	2	3
α-helix	315-317	3
β-strand	318-320	3	2
β-strand	326-328	3	2
β-strand	335-336	2	3
β-strand	343-344	2	4
α-helix	351-353	3
α-helix	356-359	4
β-strand	366-367	2	4
α-helix	369-385	17
α-helix	395-404	10
α-helix	406-407	2
α-helix	417-426	10
α-helix	435-436	2
α-helix	437-440	4
α-helix	444-447	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calcium/calmodulin-dependent protein kinase kinase 2	A	protein	298	Homo sapiens	Q96RR4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YVB_1 Calcium/calmodulin-dependent protein kinase kinase 2 (chains A)
GSSGSSGDCVQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRR
PPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELV
NQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIAD
FGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPF
MDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTR

Ligands and cofactors

ID	Name	Formula	Copies
92C	(3Z)-5-chloro-3-[(1-methyl-1H-pyrazol-4-yl)methylidene]-1,3-dihydro-2H-indol-2-…	C13 H10 Cl N3 O	1

Water and common crystallization additives (GOL, PGE, CL) are not listed.

Primary citation

Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method. Takaya, D., Niwa, H., Mikuni, J. et al. J Mol Graph Model (2020) 99:107599-107599. DOI 10.1016/j.jmgm.2020.107599 · PubMed

Other PDB entries of the same protein (UniProt Q96RR4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Y3O 1.5 Å, 14-3-3 Sigma in complex with phosphorylated CAMKK2 peptide
6Y8A 1.5 Å, 14-3-3 Sigma in complex with phosphorylated camkk2{pS511} peptide
8TUC 1.5 Å, Unphosphorylated CaMKK2 in complex with CC-8977
5UYJ 1.6 Å, Crystal Structure of the Human CAMKK2B
5UY6 1.7 Å, Crystal Structure of the Human CAMKK2B
6BQQ 1.8 Å, Crystal Structure of the Human CAMKK2B in complex with BI2526
5VT1 1.9 Å, Crystal Structure of the Human CAMKK2B bound to a thiadiazinone benzamide inhibitor
6BLE 1.9 Å, Crystal Structure of the Human CAMKK2B in complex with CP673451
5YV8 1.93 Å, Structure of CaMKK2 in complex with CKI-002
6BQP 1.95 Å, Crystal Structure of the Human CAMKK2B in complex with Crenolanib
6BKU 2.0 Å, Crystal Structure of the Human CAMKK2B bound to GSK650394
6BQL 2.0 Å, Crystal Structure of the Human CAMKK2B in complex with TAE-226

Browse structure collections

About this viewer

MolViewer shows 5YVB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.