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)

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), 0.203 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of JNK3 in complex with a fragment molecule

Ahn, H.-C., Duong, M.T.H.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J6F (Subject of Investigation/LOI) Query on J6F Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	7-hexyl-3-methyl-8-sulfanylidene-9H-purine-2,6-dione C₁₂ H₁₈ N₄ O₂ S UXIHCIYDMGYKSF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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), 0.203 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-26

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.