7YAW: ZAK

Crystal structure of ZAK in complex with compound YH-180. Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Aug 2023.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,900
Mol. weight: 143.98 kDa
Ligands: IGS
Released: 9 Aug 2023

Explore 7YAW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YAW contains 77 α-helices and 41 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: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	3
α-helix	13-15	3
β-strand	16-22A	7	3
β-strand	30-35	6	3
β-strand	40-47	8	3
α-helix	52-59	8
β-strand	65	1	4
α-helix	66-67	2
β-strand	68-74	7	3
β-strand	77-83	7	3
β-strand	89	1	4
α-helix	90-94	5
α-helix	97-101	5
α-helix	104-119	16
α-helix	120-124	5
α-helix	136-138	3
β-strand	139-141	3	4
β-strand	147-149	3	4
α-helix	154-157	4
α-helix	170-172	3
α-helix	175-178	4
α-helix	181-183	3
α-helix	186-201	16
α-helix	211-220	10
α-helix	225-228	4
α-helix	233-242	10
α-helix	247-249	3
α-helix	251-252	2
α-helix	253-264	12
α-helix	269-277	9
α-helix	280-297	18

Chain B: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	5
α-helix	13-15	3
β-strand	16-17	2	5
β-strand	21-22A	2	5
β-strand	30-35	6	5
β-strand	40-47	8	5
α-helix	56-59	4
β-strand	65	1	6
α-helix	66-67	2
β-strand	68-74	7	5
β-strand	77-83	7	5
β-strand	89	1	6
α-helix	90-94	5
α-helix	97-101	5
α-helix	104-119	16
α-helix	120-124	5
α-helix	136-138	3
β-strand	139-141	3	6
β-strand	147-149	3	6
α-helix	167-172	6
α-helix	175-178	4
α-helix	186-201	16
α-helix	211-220	10
α-helix	233-242	10
α-helix	247-249	3
α-helix	251-252	2
α-helix	253-264	12
α-helix	269-277	9
α-helix	280-298	19

Chain C: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	7
α-helix	13-15	3
β-strand	16-18	3	7
β-strand	29-35	7	7
β-strand	40-47	8	7
α-helix	56-58	3
β-strand	65	1	8
α-helix	66-67	2
β-strand	68-74	7	7
β-strand	77-83	7	7
β-strand	89	1	8
α-helix	90-94	5
α-helix	97-101	5
α-helix	104-119	16
α-helix	120-124	5
α-helix	136-138	3
β-strand	139-141	3	8
β-strand	147-149	3	8
α-helix	167-172	6
α-helix	175-178	4
α-helix	186-201	16
α-helix	211-220	10
α-helix	225-228	4
α-helix	233-242	10
α-helix	247-249	3
α-helix	251-252	2
α-helix	253-264	12
α-helix	269-277	9
α-helix	280-296	17

Chain D: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
α-helix	13-15	3
β-strand	16-22A	7	1
β-strand	30-35	6	1
β-strand	40-47	8	1
α-helix	52-59	8
β-strand	65	1	2
α-helix	66-67	2
β-strand	68-74	7	1
β-strand	77-83	7	1
β-strand	89	1	2
α-helix	90-94	5
α-helix	97-101	5
α-helix	104-119	16
α-helix	120-124	5
α-helix	136-138	3
β-strand	139-141	3	2
β-strand	147-149	3	2
α-helix	159-162	4
α-helix	167-172	6
α-helix	175-178	4
α-helix	186-201	16
α-helix	211-220	10
α-helix	233-242	10
α-helix	247-249	3
α-helix	251-252	2
α-helix	253-264	12
α-helix	269-277	9
α-helix	280-298	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase kinase kinase MLT	A, B, C, D	protein	310	Homo sapiens	Q9NYL2 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7YAW_1 Mitogen-activated protein kinase kinase kinase MLT (chains A, B, C, D)
GAMGSGASFVQIKFDDLQFFENCGGGSFGSVYRAKWISQDKEVAVKKLLKIEKEAEILSV
LSHRNIIQFYGVILEPPNYGIVTEYASLGSLYDYINSNRSEEMDMDHIMTWATDVAKGMH
YLHMEAPVKVIHRDLKSRNVVIAADGVLKICDFGASRFHNHTTHMSLVGTFPWMAPEVIQ
SLPVSETCDTYSYGVVLWEMLTREVPFKGLEGLQVAWLVVEKNERLTIPSSCPRSFAELL
HQCWEADAKKRPSFKQIISILESMSNDTSLPDKCNSFLHNKAEWRCEIEATLERLKKLER
DLSFKEQELK

Ligands and cofactors

ID	Name	Formula	Copies
IGS	~{N}-[3-[[5-[1-[2,6-bis(fluoranyl)-3-[(3-phenylphenyl)sulfonylamino]phenyl]-1,2…	C32 H28 F2 N8 O4 S	4

Primary citation

Rational Design of Covalent Kinase Inhibitors by an Integrated Computational Workflow (Kin-Cov). Zhou, Y., Yu, H., Vind, A.C. et al. J Med Chem (2023) 66:7405-7420. DOI 10.1021/acs.jmedchem.3c00088 · PubMed

Other PDB entries of the same protein (UniProt Q9NYL2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5X5O 1.87 Å, Crystal structure of ZAK in complex with compound D2829
6JUU 1.9 Å, Crystal structure of ZAK in complex with compound 6r
6JUT 2.1 Å, Crystal structure of ZAK in complex with compound 6k
5HES 2.14 Å, Human leucine zipper- and sterile alpha motif-containing kinase (ZAK, MLT, HCCS-4, MRK,…
9RPV 2.35 Å, Structure of the ZAK-bound human disome
7YAZ 2.54 Å, Crystal structure of ZAK in complex with compound YH-186
9RSX 2.91 Å, Structure of RACK1 bound to the C-terminus of SERBP1 and the RIH region of ZAK

Browse structure collections

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