3DND: PDB entry 3DND

cAMP-dependent protein kinase PKA catalytic subunit with PKI-5-24. Determined by X-ray diffraction at 2.26 Å resolution. Released 23 Jun 2009.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Bos taurus
Chains: 2
Atoms: 3,225
Mol. weight: 43.12 kDa
Ligands: LL2
Released: 23 Jun 2009

Explore 3DND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DND contains 19 α-helices and 15 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: 18 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	16-31	16
α-helix	40-42	3
β-strand	43-52	10	1
β-strand	55-62	8	1
β-strand	67-75	9	1
α-helix	76-81	6
α-helix	85-97	13
β-strand	103	1	2
α-helix	104-105	2
β-strand	106-111	6	1
β-strand	115-121	7	1
α-helix	122	1
β-strand	127	1	2
α-helix	128-135	8
α-helix	140-159	20
β-strand	162-163	2	3
α-helix	169-171	3
β-strand	172-174	3	2
β-strand	180-182	3	2
β-strand	189-190	2	3
β-strand	195	1	4
β-strand	199-200	2	5
α-helix	202-204	3
α-helix	207-210	4
β-strand	215	1	4
α-helix	218-233	16
α-helix	243-252	10
α-helix	263-272	10
α-helix	289-292	4
α-helix	295-297	3
α-helix	302-306	5
α-helix	311-312	2

Chain I: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	22-23	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-dependent protein kinase catalytic subunit alpha	A	protein	350	Bos taurus	P00517 (AlphaFold model)
cAMP-dependent protein kinase inhibitor alpha	I	protein	20		P61926 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3DND_1 cAMP-dependent protein kinase catalytic subunit alpha (chains A)
GNAAAAKKGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLV
KHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVM
EYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYI
QVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFA
DQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKDGVNDIKNHKWFATT
DWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (I), FASTA

>3DND_2 cAMP-dependent protein kinase inhibitor alpha (chains I)
TTYADFIASGRTGRRNAIHD

Ligands and cofactors

ID	Name	Formula	Copies
LL2	5-benzyl-1,3-thiazol-2-amine	C10 H10 N2 S	1

Primary citation

Crystallography-independent determination of ligand binding modes. Orts, J., Tuma, J., Reese, M. et al. Angew Chem Int Ed Engl (2008) 47:7736-7740. DOI 10.1002/anie.200801792 · PubMed

Other PDB entries of the same protein (UniProt P00517 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4Z84 1.55 Å, PKAB3 in complex with pyrrolidine inhibitor 34a
4C38 1.58 Å, PKA-S6K1 Chimera with compound 21e (CCT239066) bound
1XH8 1.6 Å, Crystal Structures of Protein Kinase B Selective Inhibitors in Complex with Protein…
5VHB 1.61 Å, Crystal structure of Protein Kinase A in complex with the PKI peptide and…
1XH9 1.64 Å, Crystal Structures of Protein Kinase B Selective Inhibitors in Complex with Protein…
3ZO4 1.65 Å, The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors
4C33 1.7 Å, PKA-S6K1 Chimera Apo
4C37 1.7 Å, PKA-S6K1 Chimera with compound 21a (CCT196539) bound
8SF8 1.7 Å, Structure of bovine PKA bound to (R)-N-(4-(1H-pyrrolo[2,3-b]pyridin-4-yl)phenyl)-2-amino-…
4C34 1.78 Å, PKA-S6K1 Chimera with Staurosporine bound
3KKV 1.8 Å, Structure of PKA with a protein Kinase B-selective inhibitor.
4Z83 1.8 Å, PKAB3 in complex with pyrrolidine inhibitor 47a

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