5R9L: Mitogen-activated protein kinase 14

PanDDA analysis group deposition Form1 MAP kinase p38-alpha -- Fragment N14274a in complex with MAP kinase p38-alpha. Determined by X-ray diffraction at 1.47 Å resolution. Released 22 Jul 2020.

Method: X-ray diffraction
Resolution: 1.47 Å
Organism: Mus musculus
Chains: 1
Atoms: 3,040
Mol. weight: 41.92 kDa
Ligands: MG, SRJ
Released: 22 Jul 2020

Explore 5R9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5R9L contains 24 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: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	8-13	6	1
β-strand	16-21	6	1
β-strand	24-29	6	2
β-strand	36-43	8	2
β-strand	49-55	7	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	112	1	3
α-helix	113-116	4
α-helix	124-143	20
α-helix	153-155	3
β-strand	156-158	3	3
β-strand	164-166	3	3
α-helix	177-179	3
α-helix	184-187	4
α-helix	191-194	4
α-helix	203-218	16
α-helix	228-239	12
α-helix	244-247	4
α-helix	253-260	8
α-helix	263-264	2
α-helix	266-268	3
α-helix	270-273	4
α-helix	279-288	10
α-helix	293-295	3
α-helix	297-298	2
α-helix	299-303	5
α-helix	306-308	3
α-helix	318-322	5
α-helix	326-329	4
α-helix	334-346	13

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

>5R9L_1 Mitogen-activated protein kinase 14 (chains A)
MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRVAVKKLSRPFQ
SIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQ
KLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMT
GYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVG
TPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAA
QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
SRJ	(3~{S})-2-(cyclopropylmethyl)-3-[(~{S})-oxidanyl(phenyl)methyl]-2-azabicyclo[2.…	C18 H25 N O2	1

Water and common crystallization additives (SO4, 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
6Y7W 1.39 Å, Fragment KCL_1337 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…

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