8X5M | pdb_00008x5m

The Crystal Structure of JNK1 from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8X5M/pdb

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


• Deposited: 2023-11-17 Released: 2023-12-27 
• Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of JNK1 from Biortus.

Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.53 kDa 
• Atom Count: 3,097 
• Modeled Residue Count: 341 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 8	A	363	Homo sapiens	Mutation(s): 0  Gene Names: MAPK8 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45983 (Homo sapiens) Explore P45983  Go to UniProtKB:  P45983
PHAROS:  P45983 GTEx:  ENSG00000107643

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y4O	B [auth A]	3-[4-(dimethylamino)butanoylamino]-~{N}-[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]benzamide C29 H31 N7 O2 JCQSXSKNIVAALC-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.17	α = 90
b = 128.405	β = 90
c = 82.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Li, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary