[English] 日本語
Yorodumi
- PDB-9nbx: Crystal structure of PAK1 bound to C2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nbx
TitleCrystal structure of PAK1 bound to C2
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / Kinase / inhibitor
Function / homology
Function and homology information


negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of fibroblast migration / regulation of axonogenesis / RHOV GTPase cycle / positive regulation of intracellular estrogen receptor signaling pathway / branching morphogenesis of an epithelial tube / establishment of cell polarity / RHOJ GTPase cycle / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / exocytosis / Fc-gamma receptor signaling pathway involved in phagocytosis / RHO GTPases activate PAKs / glutathione transferase / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / glutathione transferase activity / intercalated disc / Sema3A PAK dependent Axon repulsion / Smooth Muscle Contraction / positive regulation of protein targeting to membrane / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / positive regulation of axon extension / positive regulation of vascular associated smooth muscle cell proliferation / RHO GTPases activate PKNs / collagen binding / positive regulation of stress fiber assembly / neuron projection morphogenesis / ruffle / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / glutathione metabolic process / CD209 (DC-SIGN) signaling / cellular response to starvation / cerebellum development / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / MAPK6/MAPK4 signaling / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / wound healing / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cellular response to insulin stimulus / G beta:gamma signalling through CDC42 / cell migration / cell-cell junction / lamellipodium / chromosome / actin cytoskeleton organization / nuclear membrane / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / chromatin remodeling / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / dendrite / centrosome / DNA damage response / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Glutathione S-transferase class-mu 26 kDa isozyme / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, W. / Oh, A. / Kiefer, J.R. / Hsu, P.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J.Chem.Inf.Model. / Year: 2025
Title: Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions.
Authors: Walters, B.T. / Patapoff, A.W. / Kiefer, J.R. / Wu, P. / Wang, W.
History
DepositionFeb 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1
B: Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5385
Polymers122,6692
Non-polymers8693
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.818, 81.359, 65.854
Angle α, β, γ (deg.)90.00, 106.99, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1 / GST 26 / Sj26 antigen / SjGST / Alpha-PAK / p21-activated kinase 1 / PAK-1 / p65-PAK


Mass: 61334.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: Q13153, glutathione transferase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1BW5 / (6M)-8-(3-aminopropyl)-6-(4-butoxy-2-methylphenyl)-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one


Mass: 395.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium Sulfate, 0.1M Tris pH8.5, 30% PEG 4000

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 33900 / % possible obs: 97.8 % / Redundancy: 3.1 % / CC1/2: 0.996 / Rrim(I) all: 0.048 / Χ2: 1.006 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.60.50816690.570.8520.3590.6250.9397.6
2.19-2.232.70.48816980.60.8660.3390.5961.01298.4
2.23-2.272.80.42916890.710.9110.2920.5211.05698.7
2.27-2.322.80.38717200.7640.9310.2660.4721.06198.5
2.32-2.372.90.30616720.870.9650.2080.372198.6
2.37-2.4230.2817050.9080.9760.1870.3381.06498.7
2.42-2.4830.23917190.9220.980.1580.2881.08999
2.48-2.5530.20617160.9310.9820.1370.2481.13199.2
2.55-2.6230.17317040.9620.990.1140.2081.17398.7
2.62-2.713.10.14517210.9710.9930.0940.1741.11399.5
2.71-2.813.20.12117100.9810.9950.0780.1451.14599.7
2.81-2.923.20.10817320.9830.9960.0690.1291.16299.3
2.92-3.053.30.09617190.9860.9970.0610.1151.02399.6
3.05-3.213.30.08117300.9920.9980.0510.0960.95799.7
3.21-3.413.40.0717260.9910.9980.0440.0830.89599.8
3.41-3.683.30.06217360.9920.9980.0390.0730.79499.3
3.68-4.053.30.06916850.990.9980.0440.0820.94297.4
4.05-4.633.20.06916240.9860.9970.0460.0831.0893.4
4.63-5.833.20.05816710.9890.9970.0380.0690.92794.9
5.83-503.20.0415540.9960.9990.0260.0480.60586.4

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→31.93 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1662 4.99 %
Rwork0.2246 --
obs0.2267 33297 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→31.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 0 62 41 4342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064369
X-RAY DIFFRACTIONf_angle_d0.7175922
X-RAY DIFFRACTIONf_dihedral_angle_d13.526601
X-RAY DIFFRACTIONf_chiral_restr0.049692
X-RAY DIFFRACTIONf_plane_restr0.01751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.3821480.32862614X-RAY DIFFRACTION98
2.21-2.280.31131210.29692685X-RAY DIFFRACTION99
2.28-2.370.28631300.26712631X-RAY DIFFRACTION99
2.37-2.460.2721490.25592650X-RAY DIFFRACTION99
2.46-2.570.31361410.25052653X-RAY DIFFRACTION99
2.57-2.710.27941340.24962678X-RAY DIFFRACTION99
2.71-2.880.31991420.24982647X-RAY DIFFRACTION100
2.88-3.10.31171570.23952685X-RAY DIFFRACTION100
3.1-3.410.29941350.23832687X-RAY DIFFRACTION100
3.41-3.90.23541430.20042670X-RAY DIFFRACTION99
3.91-4.920.22541370.19262529X-RAY DIFFRACTION94
4.92-31.930.24581250.2132506X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8587-0.2940.23870.4220.20560.7269-0.28620.3972-0.6494-0.26570.10010.2660.6086-0.521600.9081-0.00670.13290.8628-0.09020.927483.9991-23.47797.9763
23.77340.4603-2.10182.4584-0.00835.5079-0.0583-0.20870.0552-0.0106-0.0634-0.0746-0.44280.812-0.00030.4058-0.0285-0.06630.4941-0.01130.363985.7386-1.26421.4141
30.56960.7720.48091.07960.42721.2371-0.0316-0.16710.1520.42140.08410.21130.3944-0.31690.00010.6665-0.02980.03970.6603-0.07940.777859.2098-16.7098-16.0152
41.27320.61390.38822.2557-0.48392.2313-0.17240.156-0.11750.18740.05750.09540.2179-0.205400.4135-0.00540.02590.4222-0.05370.506871.4391-3.6015-20.3852
50.71260.11290.09090.4282-0.39771.22410.0129-0.5005-0.1140.42170.01810.1322-0.0574-0.11130.00020.56080.02940.03080.5491-0.05540.507374.63383.6649-8.9479
60.17770.0490.23810.04370.10750.32980.0768-0.0827-0.02490.45190.0363-0.3850.31250.84710.00010.69380.0396-0.00590.8066-0.09830.674687.93938.4432-10.1794
72.58911.1542-0.66840.8398-0.17551.8318-0.02690.14720.5070.15250.13870.2074-0.348-0.0723-0.00020.42230.0388-0.05070.4118-0.00910.538977.0397.5353-24.2468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 249 through 345 )
2X-RAY DIFFRACTION2chain 'A' and (resid 346 through 541 )
3X-RAY DIFFRACTION3chain 'B' and (resid 254 through 336 )
4X-RAY DIFFRACTION4chain 'B' and (resid 337 through 402 )
5X-RAY DIFFRACTION5chain 'B' and (resid 403 through 459 )
6X-RAY DIFFRACTION6chain 'B' and (resid 460 through 491 )
7X-RAY DIFFRACTION7chain 'B' and (resid 492 through 542 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more