5WP1: Complex of ERK2 with 5,7-dihydroxychromone

Complex of ERK2 with 5,7-dihydroxychromone. Determined by X-ray diffraction at 1.4 Å resolution. Released 8 Aug 2018.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,199
Mol. weight: 41.8 kDa
Ligands: BEZ, B7S
Released: 8 Aug 2018

Explore 5WP1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WP1 contains 23 α-helices and 13 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	1
β-strand	37-44	8	1
β-strand	49-56	8	1
α-helix	62-77	16
β-strand	83	1	2
β-strand	88-90	3	1
β-strand	101-106	6	1
β-strand	110-111	2	2
α-helix	112-118	7
α-helix	120-122	3
α-helix	123-142	20
β-strand	145-146	2	3
α-helix	152-154	3
β-strand	155-157	3	2
β-strand	163-165	3	2
β-strand	172-173	2	3
α-helix	176-178	3
β-strand	180	1	4
α-helix	191-193	3
α-helix	196-199	4
β-strand	202	1	4
α-helix	208-223	16
α-helix	233-244	12
α-helix	247-248	2
α-helix	249-253	5
α-helix	258-266	9
α-helix	268-269	2
α-helix	271-274	4
α-helix	275-278	4
α-helix	284-293	10
α-helix	302-303	2
α-helix	304-308	5
α-helix	311-313	3
α-helix	319-321	3
α-helix	340-350	11
α-helix	352-354	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 1	A	protein	357	Homo sapiens	P28482 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5WP1_1 Mitogen-activated protein kinase 1 (chains A)
AAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQT
YCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSN
DHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGF
LTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGI
LGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIE
VEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS

Ligands and cofactors

ID	Name	Formula	Copies
BEZ	Benzoic acid	C7 H6 O2	1
B7S	5,7-dihydroxy-4H-1-benzopyran-4-one	C9 H6 O4	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Multiple phytochemicals at low doses accumulatively inhibit one key protein in cancers. Shin, S.H., Malakhova, M., Kurinov, I. et al. To be published.

Other PDB entries of the same protein (UniProt P28482 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8AOJ 1.12 Å, Specific covalent inhibitor of ERK2
4ZZN 1.33 Å, Human ERK2 in complex with an inhibitor
6SLG 1.33 Å, Human ERK2 with ERK1/2 inhibitor, AZD0364.
4QTA 1.45 Å, Structure of human ERK2 in complex with SCH772984 revealing a novel inhibitor-induced…
4QTE 1.5 Å, Structure of ERK2 in complex with VTX-11e, 4-{2-[(2-CHLORO-4-FLUOROPHENYL)AMINO]-5-METHYL…
2Y9Q 1.55 Å, Crystal structure of human ERK2 complexed with a MAPK docking peptide
6QA3 1.57 Å, ERK2 mini-fragment binding
6QAL 1.57 Å, ERK2 mini-fragment binding
6GJD 1.58 Å, Erk2 signalling protein
6QA1 1.58 Å, ERK2 mini-fragment binding
6QAH 1.58 Å, ERK2 mini-fragment binding
6QAQ 1.58 Å, ERK2 mini-fragment binding

Browse structure collections

About this viewer

MolViewer shows 5WP1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.