7YL1 | pdb_00007yl1

Crystal structure of JNK3 in complex with a fragment molecule

• PDB DOI: https://doi.org/10.2210/pdb7YL1/pdb

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


• Deposited: 2022-07-25 Released: 2023-07-26 
• Deposition Author(s): Ahn, H.-C., Duong, M.T.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of JNK3 in complex with a fragment molecule

Ahn, H.-C., Duong, M.T.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 52.93 kDa 
• Atom Count: 2,925 
• Modeled Residue Count: 352 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 10	A	464	Homo sapiens	Mutation(s): 0  Gene Names: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P53779 (Homo sapiens) Explore P53779  Go to UniProtKB:  P53779
PHAROS:  P53779 GTEx:  ENSG00000109339

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J6F (Subject of Investigation/LOI)	B [auth A]	7-hexyl-3-methyl-8-sulfanylidene-9H-purine-2,6-dione C12 H18 N4 O2 S UXIHCIYDMGYKSF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.149	α = 90
b = 71.985	β = 90
c = 107.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Ahn, H.-C., Duong, M.T.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2018R1D1A1B07050975
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1F1A1063558

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary