5V62: Phospho-ERK2

Phospho-ERK2 bound to bivalent inhibitor SBP3. Determined by X-ray diffraction at 1.9 Å resolution. Released 26 Jul 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,411
Mol. weight: 44.3 kDa
Ligands: AKS, FRZ
Released: 26 Jul 2017

Explore 5V62 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V62 contains 30 α-helices and 13 β-strands across 2 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: 27 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	1
β-strand	17-19	3	1
β-strand	25-33	9	2
β-strand	38-44	7	2
β-strand	49-56	8	2
α-helix	62-77	16
β-strand	83	1	3
α-helix	84-86	3
β-strand	88-90	3	2
α-helix	95-97	3
β-strand	101-106	6	2
α-helix	107-108	2
β-strand	110-111	2	3
α-helix	112-118	7
α-helix	120-122	3
α-helix	123-142	20
β-strand	145-146	2	4
α-helix	152-154	3
β-strand	155-157	3	3
β-strand	163-165	3	3
β-strand	172-173	2	4
α-helix	185	1
α-helix	191-193	3
α-helix	196-200	5
α-helix	208-223	16
α-helix	233-244	12
α-helix	247-248	2
α-helix	249-252	4
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	331-334	4
α-helix	340-351	12
α-helix	352-354	3

Chain I: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	714-716	3
α-helix	717-719	3
α-helix	721-725	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 1	A	protein	351	Homo sapiens	P28482 (AlphaFold model)
Ribosomal protein S6 kinase alpha-1	I	protein	21	Homo sapiens	Q15418 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5V62_1 Mitogen-activated protein kinase 1 (chains A)
GPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTL
REIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYF
LYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVA
TRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQ
EDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALA
HPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS

Sequence of entity 2 (I), FASTA

>5V62_2 Ribosomal protein S6 kinase alpha-1 (chains I)
KGTAQLKPIESSILAQRRVRK

Ligands and cofactors

ID	Name	Formula	Copies
AKS	N-(hex-5-yn-1-yl)hexanamide	C12 H21 N O	1
FRZ	5-(2-PHENYLPYRAZOLO[1,5-a]pyridin-3-yl)-1H-PYRAZOLO[3,4-c]pyridazin-3-amine	C18 H13 N7	1

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

Primary citation

Structure-Guided Strategy for the Development of Potent Bivalent ERK Inhibitors. Lechtenberg, B.C., Mace, P.D., Sessions, E.H. et al. ACS Med Chem Lett (2017) 8:726-731. DOI 10.1021/acsmedchemlett.7b00127 · PubMed

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.
5WP1 1.4 Å, Complex of ERK2 with 5,7-dihydroxychromone
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

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