5D9K: Rsk2 N-terminal Kinase

Rsk2 N-terminal Kinase in Complex with BI-D1870. Determined by X-ray diffraction at 2.55 Å resolution. Released 2 Sept 2015.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,599
Mol. weight: 76.93 kDa
Ligands: 584
Released: 2 Sept 2015

Explore 5D9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D9K contains 30 α-helices and 24 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: 16 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	65-67	3
β-strand	68-76	9	1
β-strand	81-87	7	1
β-strand	89	1	2
β-strand	96-103	8	1
α-helix	109-124	16
β-strand	130	1	3
α-helix	131-132	2
β-strand	133-138	6	1
β-strand	142-147	6	1
β-strand	153-154	2	3
α-helix	155-162	8
α-helix	167-186	20
β-strand	190-191	2	4
α-helix	196-198	3
β-strand	199-201	3	3
β-strand	207-209	3	3
β-strand	214-215	2	4
α-helix	232-234	3
α-helix	237-240	4
α-helix	247-263	17
α-helix	273-282	10
α-helix	283-285	3
α-helix	293-302	10
α-helix	318-322	5
α-helix	325-327	3
α-helix	332-336	5
α-helix	341-342	2

Chain B: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	65-67	3
β-strand	68-76	9	5
β-strand	81-87	7	5
β-strand	90	1	2
β-strand	96-103	8	5
α-helix	111-124	14
β-strand	130	1	6
β-strand	133-138	6	5
β-strand	142-147	6	5
β-strand	153-154	2	6
α-helix	155-162	8
α-helix	167-186	20
β-strand	189-191	3	7
α-helix	196-198	3
β-strand	199-201	3	6
β-strand	207-209	3	6
β-strand	214-216	3	7
α-helix	232-234	3
α-helix	237-240	4
α-helix	247-263	17
α-helix	273-282	10
α-helix	293-302	10
α-helix	318-322	5
α-helix	325-327	3
α-helix	332-336	5
α-helix	341-342	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosomal protein S6 kinase alpha-3	A, B	protein	330	Homo sapiens	P51812 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5D9K_1 Ribosomal protein S6 kinase alpha-3 (chains A, B)
GPNPQTEEVSIKEIAITHHVKEGHEKADPSQFELLKVLGQGSFGKVFLVKKISGSDARQL
YAMKVLKKATLKVRDRVRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDLF
TRLSKEVMFTEEDVKFYLAELALALDHLHSLGIIYRDLKPENILLDEEGHIKLTDFGLSK
ESIDHEKKAYSFCGTVEYMAPEVVNRRGHTQSADWWSFGVLMFEMLTGTLPFQGKDRKET
MTMILKAKLGMPQFLSPEAQSLLRMLFKRNPANRLGAGPDGVEEIKRHSFFSTIDWNKLY
RREIHPPFKPATGRPEDTFYFDPEFTAKTP

Ligands and cofactors

ID	Name	Formula	Copies
584	(7R)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-5,7-dimethyl-8-(3-methylbutyl)-7,8…	C19 H23 F2 N5 O2	2

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

Primary citation

Discovery of Potent and Selective RSK Inhibitors as Biological Probes. Jain, R., Mathur, M., Lan, J. et al. J Med Chem (2015) 58:6766-6783. DOI 10.1021/acs.jmedchem.5b00450 · PubMed

Other PDB entries of the same protein (UniProt P51812 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NW6 1.74 Å, Rsk2 N-terminal kinase in complex with 2-amino-7-substituted benzoxazole compound 27
8EQ5 1.8 Å, Crystal structure of the N-terminal kinase domain of RSK2 in complex with SPRED2 (131-160)
4NW5 1.94 Å, Rsk2 N-terminal kinase in complex with 2-amino-7-substituted benzoxazole compound 8
5D9L 2.15 Å, Rsk2 N-terminal Kinase in Complex with bis-phenol pyrazole
8R58 2.31 Å, The RSK 2 N-terminal kinase domain in complex with BMF (1-19)
4NUS 2.39 Å, Rsk2 N-terminal kinase in complex with LJH685
4D9T 2.4 Å, Rsk2 C-terminal Kinase Domain with inhibitor (E)-methyl…
4D9U 2.4 Å, Rsk2 C-terminal Kinase Domain, (E)-tert-butyl 3-(4-amino-7-(3-hydroxypropyl)-5-p-tolyl-7H…
4JG6 2.6 Å, RSK2 CTD bound to 2-cyano-3-(1H-indazol-5-yl)acrylamide
8XEY 2.65 Å, The Crystal Structure of C-terminal kinase domain of RSK2 from Biortus
7OPO 2.75 Å, RSK2 N-terminal kinase domain in complex with ORF45
4JG7 3.0 Å, Structure of RSK2 CTD bound to 3-(3-(1H-pyrrolo[2,3-b]pyridine-3-carbonyl)phenyl)-2-cyano…

Browse structure collections

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