8YHK | pdb_00008yhk

The Crystal Structure of P21-Activated Kinases Pak4 from Biortus

PDB DOI: https://doi.org/10.2210/pdb8YHK/pdb

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

Deposited: 2024-02-28 Released: 2024-03-13
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Qi, J., Wu, B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.319 (Depositor), 0.300 (DCC)
R-Value Work:
0.249 (Depositor), 0.260 (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

The Crystal Structure of P21-Activated Kinases Pak4 from Biortus

Wang, F., Cheng, W., Lv, Z., Qi, J., Wu, B.

To be published.

Macromolecule Content

Total Structure Weight: 34.16 kDa
Atom Count: 2,349
Modeled Residue Count: 294
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 4	A	301	Homo sapiens	Mutation(s): 0 Gene Names: PAK4, KIAA1142 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens) Explore O96013 Go to UniProtKB: O96013
PHAROS: O96013 GTEx: ENSG00000130669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O96013
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE (Subject of Investigation/LOI) Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-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: 3.30 Å
R-Value Free: 0.319 (Depositor), 0.300 (DCC)
R-Value Work: 0.249 (Depositor), 0.260 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.274	α = 90
b = 146.274	β = 90
c = 43.68	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	China	--

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release

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.