9BLH: PDB entry 9BLH

Crystal structure of calcium/calmodulin-dependent protein kinase type II subunit delta complexed with ribociclib. Determined by X-ray diffraction at 2.35 Å resolution. Released 7 May 2025.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,788
Mol. weight: 69.23 kDa
Ligands: 6ZZ
Released: 7 May 2025

Explore 9BLH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BLH contains 30 α-helices and 26 β-strands across 2 chains. 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: 17 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	14-22	9	1
β-strand	26-33	8	1
β-strand	39-46	8	1
α-helix	52-67	16
β-strand	73	1	2
α-helix	74-75	2
β-strand	76-81	6	1
β-strand	85-91	7	1
β-strand	97	1	2
α-helix	98-102	5
α-helix	110-129	20
β-strand	132-133	2	3
α-helix	139-141	3
β-strand	142-144	3	2
α-helix	151-152	2
β-strand	153-155	3	2
β-strand	162-163	2	3
β-strand	170	1	4
α-helix	178-180	3
α-helix	183-186	4
β-strand	191	1	4
α-helix	194-209	16
α-helix	219-228	10
α-helix	237-240	4
α-helix	243-252	10
α-helix	261-262	2
α-helix	263-266	4
α-helix	270-273	4
α-helix	275-278	4
α-helix	285-300	16

Chain B: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	14-22	9	5
β-strand	26-33	8	5
β-strand	39-46	8	5
α-helix	52-67	16
β-strand	73	1	6
β-strand	76-81	6	5
β-strand	85-91	7	5
β-strand	97	1	6
α-helix	98-103	6
α-helix	110-129	20
β-strand	132-133	2	7
α-helix	139-141	3
β-strand	142-144	3	6
β-strand	153-155	3	6
β-strand	162-163	2	7
β-strand	170	1	8
α-helix	183-187	5
β-strand	191	1	8
α-helix	194-209	16
α-helix	219-228	10
α-helix	243-252	10
α-helix	261-262	2
α-helix	263-267	5
α-helix	270-273	4
α-helix	275-278	4
α-helix	285-297	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calcium/calmodulin-dependent protein kinase type II subunit delta	A, B	protein	300	Homo sapiens	Q13557 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9BLH_1 Calcium/calmodulin-dependent protein kinase type II subunit delta (chains A, B)
FTDEYQLFEELGKGAFSVVRRCMKIPTGQEYAAKIINTKKLSARDHQKLEREARICRLLK
HPNIVRLHDSISEEGFHYLVFDLVTGGELFEDIVAREYYSEADASHCIQQILESVNHCHL
NGIVHRDLKPENLLLASKSKGAAVKLADFGLAIEVQGDQQAWFGFAGTPGYLSPEVLRKD
PYGKPVDMWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLI
NKMLTINPAKRITASEALKHPWICQRSTVASMMHRQETVDCLKKFNARRKLKGAILTTML

Ligands and cofactors

ID	Name	Formula	Copies
6ZZ	7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo…	C23 H30 N8 O	2

Primary citation

Bacterial ubiquitin ligase engineered for small molecule and protein target identification. Ye, J.S., Majumdar, A., Park, B.C. et al. EMBO J (2026) 45:1024-1050. DOI 10.1038/s44318-025-00665-0 · PubMed

Other PDB entries of the same protein (UniProt Q13557 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3GP2 1.46 Å, Calmodulin bound to peptide from calmodulin kinase II (CaMKII)
7ZRQ 1.68 Å, 1.68 Angstrom crystal structure of Ca/CaM-E140G:CaMKIIdelta peptide complex
2WEL 1.9 Å, Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta…
5VLO 2.05 Å, The structure of human CamKII with bound inhibitor
6AYW 2.05 Å, The structure of human CamKII with bound inhibitor
2VN9 2.3 Å, Crystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform…
7ZRP 2.65 Å, 2.65 Angstrom crystal structure of Ca/CaM:CaMKIIdelta peptide complex
2W2C 2.7 Å, Structure of the tetradecameric oligomerisation domain of calcium- calmodulin dependent…

Browse structure collections

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