9P6A: The catalytic domain of MEKK2

The catalytic domain of MEKK2 in complex with ponatinib. Determined by X-ray diffraction at 2.4 Å resolution. Released 26 Nov 2025.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,108
Mol. weight: 68.6 kDa
Ligands: 0LI
Released: 26 Nov 2025

Explore 9P6A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P6A contains 28 α-helices and 19 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: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	356-365	10	1
β-strand	368-375	8	1
β-strand	381-388	8	1
α-helix	398-410	13
β-strand	418	1	2
α-helix	419-420	2
β-strand	421-427	7	1
β-strand	432-438	7	1
β-strand	443-444	2	2
α-helix	445-452	8
α-helix	455-456	2
α-helix	457-476	20
α-helix	486-488	3
β-strand	489-491	3	2
β-strand	497-499	3	2
α-helix	530-533	4
α-helix	541-556	16
α-helix	566-575	10
α-helix	588-597	10
α-helix	601-603	3
α-helix	604-606	3
α-helix	607-610	4
α-helix	614-616	3

Chain B: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	348	1	3
β-strand	356-363	8	3
β-strand	370-375	6	3
β-strand	381-388	8	3
α-helix	397-410	14
β-strand	418	1	4
α-helix	419-420	2
β-strand	421-427	7	3
β-strand	432-438	7	3
β-strand	443-444	2	4
α-helix	445-452	8
α-helix	455-456	2
α-helix	457-476	20
α-helix	486-488	3
β-strand	489-491	3	4
β-strand	497-499	3	4
α-helix	530-533	4
α-helix	540-556	17
α-helix	566-575	10
α-helix	588-597	10
α-helix	601-603	3
α-helix	604-606	3
α-helix	607-610	4
α-helix	614-616	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase kinase kinase 2	A, B	protein	299	Homo sapiens	Q9Y2U5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9P6A_1 Mitogen-activated protein kinase kinase kinase 2 (chains A, B)
GAMGRIRRRGSDIDNPTLTVMDISPPSRSPRAPTNWRLGKLLGQGAFGRVYLCYDVDTGR
ELAVKQVQFDPDSPETSKEVNALECEIQLLKNLLHERIVQYYGCLRDPQEKTLSIFMEYM
PGGSIKDQLKAYGALTENVTRKYTRQILEGVHYLHSNMIVHRDIKGANILRDSTGNVKLG
DFGASKRLQTICLSGTGMKSVTGTPYWMSPEVISGEGYGRKADIWSVACTVVEMLTEKPP
WAEFEAMAAIFKIATQPTNPKLPPHVSDYTRDFLKRIFVEAKLRPSADELLRHMFVHYH

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

Primary citation

Structural basis for MEKK2 dimerization and substrate recognition. Vish, K.J., Huet-Calderwood, C., Ha, B.H. et al. Nat Commun (2025) 17:193-193. DOI 10.1038/s41467-025-66884-5 · PubMed

Other PDB entries of the same protein (UniProt Q9Y2U5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6LDW 1.6 Å, Structure of antibody C9 in complex with methylated peptide
5HQ8 1.72 Å, Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A
2NPT 1.75 Å, Crystal Structure of the complex of human mitogen activated protein kinase kinase 5 phox…
6LDY 1.77 Å, Structure antibody D6 in complex with methylated peptide
6LDX 1.8 Å, Structure antibody E6 in complex with methylated peptide
6LDV 1.9 Å, Structure antibody F9 in complex with methylated peptide
5EX0 2.7 Å, Crystal structure of human SMYD3 in complex with a MAP3K2 peptide
2CU1 Solution structure of the PB1 domain of human protein kinase MEKK2b

Browse structure collections

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