6YZ4: PDB entry 6YZ4

Crystal structure of MKK7 (MAP2K7) with ibrutinib bound at allosteric site. Determined by X-ray diffraction at 1.7 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,727
Mol. weight: 36.26 kDa
Ligands: 1E8
Released: 12 Aug 2020

Explore 6YZ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YZ4 contains 19 α-helices and 11 β-strands across 1 chain. 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: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	120-124	5	1
β-strand	127-131	5	1
α-helix	133-135	3
β-strand	136-141	6	2
β-strand	150-155	6	2
β-strand	160-168	9	2
α-helix	173-187	15
β-strand	195	1	3
α-helix	196-197	2
β-strand	198-203	6	2
β-strand	207-213	7	2
α-helix	214-215	2
β-strand	217-218	2	3
α-helix	219-226	8
α-helix	229-231	3
α-helix	232-253	22
α-helix	262-264	3
β-strand	265-267	3	3
β-strand	273-275	3	3
α-helix	297-299	3
α-helix	302-305	4
α-helix	317-333	17
α-helix	344-353	10
α-helix	355-356	2
α-helix	358-360	3
α-helix	367-376	10
α-helix	381-383	3
α-helix	387-390	4
α-helix	394-401	8
α-helix	406-416	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dual specificity mitogen-activated protein kinase kinase 7	A	protein	307	Homo sapiens	O14733 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YZ4_1 Dual specificity mitogen-activated protein kinase kinase 7 (chains A)
SMKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKE
ENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERI
LGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSA
GCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQE
EPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVM
AKTESPR

Ligands and cofactors

ID	Name	Formula	Copies
1E8	1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperid…	C25 H24 N6 O2	1

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

Primary citation

Catalytic Domain Plasticity of MKK7 Reveals Structural Mechanisms of Allosteric Activation and Diverse Targeting Opportunities. Schroder, M., Tan, L., Wang, J. et al. Cell Chem Biol (2020) 27:1285-1295.e4. DOI 10.1016/j.chembiol.2020.07.014 · PubMed

Other PDB entries of the same protein (UniProt O14733 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5Y90 1.3 Å, MAP2K7 mutant -C218S
6YFZ 1.9 Å, Crystal structure of MKK7 (MAP2K7), apo form
7OVI 1.95 Å, Protein kinase MKK7 in complex with phenethyltriazole-substituted pyrazolopyrimidine
6YG0 2.0 Å, Crystal structure of S287D,T291D MKK7 (MAP2K7), apo form
6YG2 2.0 Å, Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and…
6YG3 2.05 Å, Crystal structure of MKK7 (MAP2K7) covalently bound with CPT1-70-1
7OVK 2.05 Å, Protein kinase MKK7 in complex with 5-bromo-2-hydroxyphenyl-substituted pyrazolopyrimidine
7CBX 2.06 Å, Crystal structure of MAP2K7 complexed with a covalent inhibitor 12
5B2L 2.1 Å, A crucial role of Cys218 in the stabilization of an unprecedented auto-inhibition form…
6IB2 2.1 Å, The structure of MKK7 in complex with the covalent 4-amino-pyrazolopyrimidine 4a
6QG7 2.1 Å, Structure of the mitogen activated kinase kinase 7 in complex with pyrazolopyrimidine 1k
6YG6 2.15 Å, Crystal structure of MKK7 (MAP2K7) covalently bound with type-II inhibitor TL10-105

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