6Y7W: Fragment KCL_1337

Fragment KCL_1337 in complex with MAP kinase p38-alpha. Determined by X-ray diffraction at 1.39 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 1.39 Å
Organism: Mus musculus
Chains: 1
Atoms: 3,160
Mol. weight: 42.4 kDa
Ligands: SB4, CA, OFW
Released: 11 Mar 2020

Explore 6Y7W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y7W contains 23 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: 23 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	1
β-strand	16-21	6	1
β-strand	24-33	10	2
β-strand	36-43	8	2
β-strand	48-55	8	2
α-helix	62-77	16
β-strand	83	1	3
β-strand	88-90	3	2
α-helix	96-98	3
β-strand	103-107	5	2
β-strand	111-112	2	3
α-helix	113-115	3
α-helix	124-143	20
α-helix	153-155	3
β-strand	156-158	3	3
β-strand	164-166	3	3
α-helix	191-194	4
α-helix	204-218	15
α-helix	228-239	12
α-helix	241-243	3
α-helix	244-247	4
α-helix	253-261	9
α-helix	263-264	2
α-helix	266-269	4
α-helix	270-272	3
α-helix	279-288	10
α-helix	297-298	2
α-helix	299-303	5
α-helix	306-308	3
α-helix	314-316	3
α-helix	318-322	5
α-helix	326-329	4
α-helix	334-347	14
α-helix	350-352	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 14	A	protein	360	Mus musculus	P47811 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Y7W_1 Mitogen-activated protein kinase 14 (chains A)
MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRVAVKKLSRPFQ
SIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQ
KLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDSELKILDFGLARHTDDEMT
GYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVG
TPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAA
QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES

Ligands and cofactors

ID	Name	Formula	Copies
SB4	4-(4-fluorophenyl)-1-(4-piperidinyl)-5-(2-amino-4-pyrimidinyl)-imidazole	C18 H19 F N6	1
CA	Calcium ion	Ca	4
OFW	(2~{R})-~{N}-[(2-azanyl-2-adamantyl)methyl]-4-[6-[2,5-bis(oxidanylidene)pyrroli…	C26 H35 N5 O6 S	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1 beta-IL1R and p38 alpha-TAB1 Complexes. Nichols, C., Ng, J., Keshu, A. et al. J Med Chem (2020) 63:7559-7568. DOI 10.1021/acs.jmedchem.0c00403 · PubMed

Other PDB entries of the same protein (UniProt P47811 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6SP9 1.22 Å, Fragment KCL802 in complex with MAP kinase p38-alpha
6Y80 1.24 Å, Fragment KCL_916 in complex with MAP kinase p38-alpha
6SOV 1.31 Å, Fragments KCL_615 and KCL_802 in complex with MAP kinase p38-alpha
6YCW 1.34 Å, Fragment KCL_K767 in complex with MAP kinase p38-alpha
6Y7Z 1.35 Å, Fragment KCL_914 in complex with MAP kinase p38-alpha
6YCU 1.35 Å, Fragment KCL_K777 in complex with MAP kinase p38-alpha
6Y8H 1.37 Å, Novel p38-alpha crystal lattice with highly exposed p38/TAB1 non-canonical PPI surface.
6SPL 1.38 Å, Fragment KCL615 in complex with MAP kinase p38-alpha
5R97 1.44 Å, PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N13662a in…
6Y82 1.44 Å, Fragment KCL_804 in complex with MAP kinase p38-alpha
5R94 1.45 Å, PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment KCL081 in…
5R9V 1.45 Å, PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N13596a in…

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