5WP1 | pdb_00005wp1

Complex of ERK2 with 5,7-dihydroxychromone

• PDB DOI: https://doi.org/10.2210/pdb5WP1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-03 Released: 2018-08-08 
• Deposition Author(s): Kurinov, I., Malakhova, M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.180 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Multiple phytochemicals at low doses accumulatively inhibit one key protein in cancers

Shin, S.H., Malakhova, M., Kurinov, I., Lim, D.Y., Bode, A.M., Dong, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.8 kDa 
• Atom Count: 3,199 
• Modeled Residue Count: 343 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	357	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482 GTEx:  ENSG00000100030

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B7S (Subject of Investigation/LOI)	B [auth A]	5,7-dihydroxy-4H-1-benzopyran-4-one C9 H6 O4 NYCXYKOXLNBYID-UHFFFAOYSA-N
BEZ	D [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.180 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.141 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.685	α = 90
b = 69.07	β = 108.14
c = 59.845	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Kurinov, I., Malakhova, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary