4C8B: Kinase domain of human RIPK2

Structure of the kinase domain of human RIPK2 in complex with ponatinib. Determined by X-ray diffraction at 2.75 Å resolution. Released 16 Oct 2013.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 4,445
Mol. weight: 77.9 kDa
Ligands: 0LI
Released: 16 Oct 2013

Explore 4C8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4C8B contains 33 α-helices and 20 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	1
α-helix	15-17	3
β-strand	18-26	9	1
β-strand	30-37	8	1
β-strand	43-49	7	1
α-helix	56-72	17
β-strand	78	1	2
α-helix	79-80	2
β-strand	81-87	7	1
β-strand	90-96	7	1
β-strand	102	1	2
α-helix	103-108	6
α-helix	118-136	19
α-helix	141-142	2
α-helix	149-151	3
β-strand	152-154	3	2
β-strand	160-162	3	2
α-helix	190-192	3
α-helix	195-197	3
α-helix	210-224	15
α-helix	235-243	9
α-helix	262-272	11
α-helix	277-279	3
α-helix	281-282	2
α-helix	283-295	13
α-helix	300-313	14

Chain B: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	3
α-helix	15-17	3
β-strand	18-26	9	3
β-strand	31-37	7	3
β-strand	43-48	6	3
α-helix	58-72	15
β-strand	78	1	4
α-helix	79-80	2
β-strand	81-87	7	3
β-strand	90-96	7	3
β-strand	102	1	4
α-helix	103-108	6
α-helix	118-136	19
α-helix	141-142	2
α-helix	149-151	3
β-strand	152-154	3	4
β-strand	160-162	3	4
α-helix	189-192	4
α-helix	195-197	3
α-helix	202-205	4
α-helix	210-224	15
α-helix	235-243	9
α-helix	262-272	11
α-helix	277-279	3
α-helix	281-282	2
α-helix	283-295	13
α-helix	300-315	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 2	A, B	protein	334	HOMO SAPIENS	O43353 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4C8B_1 RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2 (chains A, B)
MGHHHHHHSSGVDLGTENLYFQSMSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQ
VAVKHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSL
NELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIA
DFGLSKWCMMSLSQSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVL
SRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSF
LKCLIELEPVLRTFEEITFLEAVIQLKKTKLQSV

Ligands and cofactors

ID	Name	Formula	Copies
0LI	3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)…	C29 H27 F3 N6 O	2

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

Primary citation

Inflammatory Signaling by NOD-RIPK2 Is Inhibited by Clinically Relevant Type II Kinase Inhibitors. Canning, P., Ruan, Q., Schwerd, T. et al. Chem Biol (2015) 22:1174-1184. DOI 10.1016/j.chembiol.2015.07.017 · PubMed

Other PDB entries of the same protein (UniProt O43353 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OBS 1.8 Å, Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide
9F3V 1.94 Å, RIP2K kinase domain dimer with bound compound 37 (N399), a speific NOD1 pathway inhibitor
5NG0 2.0 Å, Structure of RIP2K(L294F) with bound AMPPCP
8X2O 2.26 Å, RIPK2 in complex with K252
7OBT 2.3 Å, Crystal structure of 14-3-3 sigma in complex with RIPK2 phosphopeptide and stabilizer…
6ES0 2.38 Å, Crystal structure of the kinase domain of human RIPK2 in complex with the activation…
5AR2 2.44 Å, RIP2 Kinase Catalytic Domain (1 - 310)
5J7B 2.53 Å, The identification and pharmacological characterization of…
6HMX 2.53 Å, RIP2 Kinase Catalytic Domain complex with N(4,5dimethyl1Hpyrazol3yl)7methoxy6(2methylprop…
6SZJ 2.53 Å, RIP2 Kinase Catalytic Domain complex with 5amino1tertbutyl3(3methoxyphenyl)1H…
5NG3 2.6 Å, Structure of inactive kinase RIP2K(K47R)
6RNA 2.62 Å, RIP2 Kinase Catalytic Domain complex with 2({4[(1,3benzothiazol5yl)amino]6(2methylpropane…

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