5NG0: RIP2K(L294F) with bound AMPPCP

Structure of RIP2K(L294F) with bound AMPPCP. Determined by X-ray diffraction at 2.0 Å resolution. Released 7 Jun 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,992
Mol. weight: 70.81 kDa
Ligands: CO, MG, ACP
Released: 7 Jun 2017

Explore 5NG0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NG0 contains 34 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: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	1
α-helix	10-11	2
β-strand	12	1	2
α-helix	15-17	3
β-strand	18-26	9	2
β-strand	31-37	7	2
β-strand	43-48	6	2
α-helix	57-72	16
β-strand	78	1	3
α-helix	79-80	2
β-strand	81-87	7	2
β-strand	90-96	7	2
β-strand	102	1	3
α-helix	103-108	6
α-helix	118-136	19
α-helix	141	1
β-strand	142-143	2	4
α-helix	149-151	3
β-strand	152-154	3	3
β-strand	160-162	3	3
β-strand	169-170	2	4
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	298-299	2

Chain B: 18 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	1
α-helix	10-11	2
β-strand	12	1	5
α-helix	15-17	3
β-strand	18-26	9	5
β-strand	31-37	7	5
β-strand	43-48	6	5
α-helix	57-72	16
β-strand	78	1	6
α-helix	79-80	2
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
α-helix	141	1
β-strand	142-143	2	7
α-helix	149-151	3
β-strand	152-154	3	6
β-strand	160-162	3	6
β-strand	169-170	2	7
α-helix	184-186	3
α-helix	190-192	3
α-helix	195-197	3
α-helix	206-209	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

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>5NG0_1 Receptor-interacting serine/threonine-protein kinase 2 (chains A, B)
GAMAMNGEAICSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLL
DSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDV
AWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLSKWRMMSLS
QSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPL
QIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVFRT
FEEI

Ligands and cofactors

ID	Name	Formula	Copies
CO	Cobalt (II) ion	Co	1
MG	Magnesium ion	Mg	2
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	2

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
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…
5AR5 2.66 Å, RIP2 Kinase Catalytic Domain (1 - 310) complex with Benzimidazole

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