5NG3: Inactive kinase RIP2K(K47R)

Structure of inactive kinase RIP2K(K47R). Determined by X-ray diffraction at 2.6 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,229
Mol. weight: 141.63 kDa
Released: 28 Jun 2017

Explore 5NG3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NG3 contains 49 α-helices and 40 β-strands across 4 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: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	5
α-helix	15-17	3
β-strand	18-27	10	5
β-strand	30-37	8	5
β-strand	43-50	8	5
α-helix	57-71	15
β-strand	78	1	6
β-strand	81-87	7	5
β-strand	90-96	7	5
β-strand	102	1	6
α-helix	103-108	6
α-helix	118-136	19
β-strand	152-154	3	6
β-strand	160-162	3	6
α-helix	168-176	9
α-helix	195-198	4
α-helix	204-206	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

Chains B and D: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	3
α-helix	15-17	3
β-strand	18-27	10	3
β-strand	30-37	8	3
β-strand	43-50	8	3
α-helix	57-71	15
β-strand	78	1	4
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
β-strand	152-154	3	4
β-strand	160-162	3	4
α-helix	168-176	9
α-helix	195-198	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

Chain C: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	7
α-helix	15-17	3
β-strand	18-27	10	7
β-strand	30-37	8	7
β-strand	43-50	8	7
α-helix	57-71	15
β-strand	78	1	8
β-strand	81-87	7	7
β-strand	90-96	7	7
β-strand	102	1	8
α-helix	103-108	6
α-helix	118-136	19
β-strand	152-154	3	8
β-strand	160-162	3	8
α-helix	168-176	9
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-interacting serine/threonine-protein kinase 2	A, D	protein	304	Homo sapiens	O43353 (AlphaFold model)
Receptor-interacting serine/threonine-protein kinase 2	B, C	protein	304	Homo sapiens	O43353 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5NG3_1 Receptor-interacting serine/threonine-protein kinase 2 (chains A, D)
GAMAMNGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVRHLHIHTPLL
DSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDV
AWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLS
QSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPL
QIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRT
FEEI

Sequence of entity 2 (B, C), FASTA

>5NG3_2 Receptor-interacting serine/threonine-protein kinase 2 (chains B, C)
GAMAMNGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVRHLHIHTPLL
DSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDV
AWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLS
QSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPL
QIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRT
FEEI

Primary citation

Structures of the inactive and active states of RIP2 kinase inform on the mechanism of activation. Pellegrini, E., Signor, L., Singh, S. et al. PLoS One (2017) 12:e0177161-e0177161. DOI 10.1371/journal.pone.0177161 · 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…
6RNA 2.62 Å, RIP2 Kinase Catalytic Domain complex with 2({4[(1,3benzothiazol5yl)amino]6(2methylpropane…
5AR5 2.66 Å, RIP2 Kinase Catalytic Domain (1 - 310) complex with Benzimidazole

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