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- PDB-6fd3: Thiophosphorylated PAK3 kinase domain -

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Basic information

Entry
Database: PDB / ID: 6fd3
TitleThiophosphorylated PAK3 kinase domain
ComponentsSerine/threonine-protein kinase PAK 3
KeywordsTRANSFERASE / kinase / thiophosphorylation / complex / ADP / phosphorylated
Function / homology
Function and homology information


signal transduction => GO:0007165 / small GTPase binding => GO:0031267 / positive regulation of dendritic spine morphogenesis / regulation of actin filament polymerization / dendritic spine morphogenesis / positive regulation of fibroblast migration / stress-activated protein kinase signaling cascade / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling ...signal transduction => GO:0007165 / small GTPase binding => GO:0031267 / positive regulation of dendritic spine morphogenesis / regulation of actin filament polymerization / dendritic spine morphogenesis / positive regulation of fibroblast migration / stress-activated protein kinase signaling cascade / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of DNA biosynthetic process / regulation of axonogenesis / activation of protein kinase activity / dendrite development / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / MAP kinase kinase activity / Sema3A PAK dependent Axon repulsion / cellular response to organic cyclic compound / Generation of second messenger molecules / ephrin receptor signaling pathway / T cell costimulation / CD209 (DC-SIGN) signaling / axonogenesis / VEGFR2 mediated vascular permeability / synapse organization / MAPK6/MAPK4 signaling / SH3 domain binding / positive regulation of neuron apoptotic process / T cell receptor signaling pathway / non-specific serine/threonine protein kinase / endosome / protein serine/threonine kinase activity / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
p21-activated kinase 3, catalytic domain / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...p21-activated kinase 3, catalytic domain / p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase PAK 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 Å
AuthorsSorrell, F.J. / Wang, D. / von Delft, F. / Bountra, C. / Edwards, A.M. / Elkins, J.M.
CitationJournal: Biochem.J. / Year: 2019
Title: Solution structures and biophysical analysis of full-length group A PAKs reveal they are monomeric and auto-inhibited incis.
Authors: Sorrell, F.J. / Kilian, L.M. / Elkins, J.M.
History
DepositionDec 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3306
Polymers33,7301
Non-polymers6005
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-22 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.825, 108.825, 57.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Serine/threonine-protein kinase PAK 3 / Beta-PAK / Oligophrenin-3 / p21-activated kinase 3 / PAK-3


Mass: 33729.734 Da / Num. of mol.: 1 / Mutation: A537D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK3, OPHN3 / Production host: Escherichia coli (E. coli)
References: UniProt: O75914, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.52→54.412 Å / Num. obs: 52114 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.52-1.566.31.5538020.5130.671.692
6.8-54.46.20.0276140.9990.0120.029

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.52 Å54.41 Å
Translation1.52 Å54.41 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q4z (chain A)

3q4z


Resolution: 1.52→54.412 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1904 2627 5.09 %
Rwork0.1751 49002 -
obs0.1759 51629 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.81 Å2 / Biso mean: 29.0289 Å2 / Biso min: 12.67 Å2
Refinement stepCycle: final / Resolution: 1.52→54.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2305 0 37 276 2618
Biso mean--24.19 39.5 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062477
X-RAY DIFFRACTIONf_angle_d0.9563376
X-RAY DIFFRACTIONf_chiral_restr0.056387
X-RAY DIFFRACTIONf_plane_restr0.005435
X-RAY DIFFRACTIONf_dihedral_angle_d10.0962071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5198-1.54740.33831460.33142446259296
1.5474-1.57720.39011250.31012541266697
1.5772-1.60940.31881250.30362527265297
1.6094-1.64440.26841410.27932553269498
1.6444-1.68270.27721170.2682545266298
1.6827-1.72470.29351330.24162546267998
1.7247-1.77140.25451200.22472572269299
1.7714-1.82350.25251450.2092579272499
1.8235-1.88240.2221470.20492568271599
1.8824-1.94960.2141560.181325772733100
1.9496-2.02770.21551220.165326092731100
2.0277-2.120.19241760.162125692745100
2.12-2.23180.17221330.157926102743100
2.2318-2.37160.20561380.157525992737100
2.3716-2.55470.18021340.166225932727100
2.5547-2.81180.18261320.157626242756100
2.8118-3.21860.17441480.160626232771100
3.2186-4.05490.14251340.150826332767100
4.0549-54.44740.16761550.16226882843100
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)
17.1153-2.2883-1.68876.48311.64727.2445-0.19760.8004-0.3936-0.89960.11690.5271.2247-0.76640.10.705-0.0996-0.07290.65090.01410.4041-5.443584.2691-22.4741
22.93080.5951-1.12026.2935-0.73117.38140.12040.89120.1235-1.12950.12270.1284-0.23980.2393-0.27620.61930.0483-0.00780.4690.00960.19350.779191.433-23.4836
38.66822.42730.89045.1249-1.07176.61770.34851.25870.0706-1.03330.2488-0.5230.19310.2775-0.52430.63810.06690.13040.4598-0.0540.329110.170596.0539-22.1984
43.33181.34360.0093.2042-0.03331.7944-0.15860.2524-0.3091-0.10890.0372-0.34010.27890.18620.11640.25730.0150.10540.2324-0.01460.261718.278693.3144-10.8596
53.389-1.45532.65264.9901-4.25878.63570.56830.5798-0.7295-1.290.2589-0.10941.33090.0245-0.73770.66670.00340.07620.347-0.11430.40677.753983.9377-15.5604
64.678-0.1813-5.44468.55495.32069.38490.16270.7035-0.9545-0.3197-0.537-0.11460.886-0.68540.27480.5169-0.02290.0090.2803-0.01750.2798-0.822883.4349-12.9378
70.96750.84080.73756.31764.44896.9956-0.0890.3539-0.0619-0.7071-0.1005-0.34070.0842-0.24160.12540.31790.02170.09260.29740.0120.23850.93798.9828-9.2115
83.4094-1.04930.53384.04173.86954.5161-0.09050.5986-0.2566-0.58070.0835-0.38710.617-0.0338-0.08980.4395-0.01750.13250.2744-0.04220.23228.862194.9025-14.6156
91.41710.14050.1681.895-0.06091.24690.004-0.08-0.01770.20550.0283-0.1246-0.07330.1061-0.02920.16710.00630.00140.13490.010.14484.373196.15565.4764
106.98594.01794.93565.45194.03436.2176-0.03450.1049-0.0709-0.03640.0712-0.3039-0.20330.128-0.00440.1444-0.0030.01990.15720.03350.17388.104396.04041.8103
112.3761-3.31750.42186.54990.73911.24420.12920.2507-0.2599-0.1689-0.10370.54890.0671-0.1858-0.0480.1938-0.0052-0.02090.21240.01310.1991-11.421690.2449-6.7689
121.51330.37750.26892.8005-0.28810.80450.0608-0.0749-0.12610.21210.0140.0860.0233-0.046-0.08550.18190.00990.0150.15260.03250.1687-4.184482.29767.9611
135.75570.20964.63252.661.93554.89590.2607-0.5882-0.49751.22670.51180.24680.3013-0.3329-0.63020.54820.05150.0070.3560.07830.2605-1.903683.492222.3133
141.9580.41741.29973.32360.19083.9930.0088-0.329-0.03520.6479-0.00510.3225-0.0248-0.30860.01920.31080.03940.1160.22020.00270.1995-7.272395.905816.877
155.6219-0.3713-1.04794.96210.7184.2013-0.0362-0.21280.00890.2825-0.0093-0.5318-0.01260.39260.0080.2402-0.0401-0.07450.228-0.00240.212616.284497.31512.7471
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 260:265)A260 - 265
2X-RAY DIFFRACTION2(chain A and resid 266:272)A266 - 272
3X-RAY DIFFRACTION3(chain A and resid 273:279)A273 - 279
4X-RAY DIFFRACTION4(chain A and resid 280:312)A280 - 312
5X-RAY DIFFRACTION5(chain A and resid 313:317)A313 - 317
6X-RAY DIFFRACTION6(chain A and resid 318:324)A318 - 324
7X-RAY DIFFRACTION7(chain A and resid 325:339)A325 - 339
8X-RAY DIFFRACTION8(chain A and resid 340:354)A340 - 354
9X-RAY DIFFRACTION9(chain A and resid 355:405)A355 - 405
10X-RAY DIFFRACTION10(chain A and resid 406:422)A406 - 422
11X-RAY DIFFRACTION11(chain A and resid 423:437)A423 - 437
12X-RAY DIFFRACTION12(chain A and resid 438:492)A438 - 492
13X-RAY DIFFRACTION13(chain A and resid 493:501)A493 - 501
14X-RAY DIFFRACTION14(chain A and resid 502:535)A502 - 535
15X-RAY DIFFRACTION15(chain A and resid 536:556)A536 - 556

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