9WS6 | pdb_00009ws6

Crystal structure of AMP-PNP-bound PAK2 kinase domain containing D368N mutant

PDB DOI: https://doi.org/10.2210/pdb9WS6/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-09-12 Released: 2026-09-16
Deposition Author(s): Chen, F.Y., Hu, H.-F., Wang, J., Luo, Z.P., Wu, J.-W., Wang, Z.-X.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.195 (Depositor), 0.199 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Kinetic and structural insights into the autoactivation of PAK2 kinase domain: A research paradigm for studying self-activating enzyme

Chen, F.Y., Hu, H.-F., Wang, J., Luo, Z.P., Wu, J.-W., Wang, Z.-X.

To be published.

Macromolecule Content

Total Structure Weight: 146.15 kDa
Atom Count: 9,673
Modeled Residue Count: 1,202
Deposited Residue Count: 1,292
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PAK-2p34	A, B, C, D	323	Homo sapiens	Mutation(s): 1 Gene Names: PAK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13177 (Homo sapiens) Explore Q13177 Go to UniProtKB: Q13177
PHAROS: Q13177 GTEx: ENSG00000180370
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13177
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], L [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]