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- PDB-2cdz: CRYSTAL STRUCTURE OF THE HUMAN P21-ACTIVATED KINASE 4 IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 2cdz
TitleCRYSTAL STRUCTURE OF THE HUMAN P21-ACTIVATED KINASE 4 IN COMPLEX WITH CGP74514A
ComponentsSERINE/THREONINE-PROTEIN KINASE PAK 4
KeywordsTRANSFERASE / PROTEIN KINASE / STE20 / PAK4 / ATP-BINDING
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / : / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / : / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / cellular response to starvation / adherens junction / regulation of cell growth / positive regulation of angiogenesis / cell migration / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase 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
Chem-23D / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDebreczeni, J.E. / Ugochukwu, E. / Eswaran, J. / Filippakopoulos, P. / Das, S. / Fedorov, O. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. ...Debreczeni, J.E. / Ugochukwu, E. / Eswaran, J. / Filippakopoulos, P. / Das, S. / Fedorov, O. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / von Delft, F. / Knapp, S.
CitationJournal: Structure / Year: 2007
Title: Crystal Structures of the P21-Activated Kinases Pak4, Pak5, and Pak6 Reveal Catalytic Domain Plasticity of Active Group II Paks.
Authors: Eswaran, J. / Lee, W.H. / Debreczeni, J.E. / Filippakopoulos, P. / Turnbull, A. / Fedorov, O. / Deacon, S.W. / Peterson, J.R. / Knapp, S.
History
DepositionJan 31, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8495
Polymers34,2361
Non-polymers6134
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)145.817, 145.817, 42.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE PAK 4 / HUMAN P21-ACTIVATED KINASE 4


Mass: 34235.691 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 291-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6B-C001 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O96013, EC: 2.7.1.37
#2: Chemical ChemComp-23D / N2-[(1R,2S)-2-AMINOCYCLOHEXYL]-N6-(3-CHLOROPHENYL)-9-ETHYL-9H-PURINE-2,6-DIAMINE


Mass: 385.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24ClN7
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 64.8 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.542
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 17, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23590 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 6.76 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.9
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.67 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVA

2bva


Resolution: 2.3→103.14 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.088 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1060 5.1 %RANDOM
Rwork0.2 ---
obs0.202 19821 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2---1.56 Å20 Å2
3---3.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→103.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2246 0 38 117 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222356
X-RAY DIFFRACTIONr_bond_other_d0.0010.021604
X-RAY DIFFRACTIONr_angle_refined_deg1.4323210
X-RAY DIFFRACTIONr_angle_other_deg0.9413.0013894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3623.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22615.037401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7331520
X-RAY DIFFRACTIONr_chiral_restr0.070.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined0.1920.2484
X-RAY DIFFRACTIONr_nbd_other0.1970.21696
X-RAY DIFFRACTIONr_nbtor_refined0.170.21135
X-RAY DIFFRACTIONr_nbtor_other0.0890.21229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.71331601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55852370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4837973
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1711836
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.382 105
Rwork0.234 1413
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)
13.82550.68781.43031.32290.26393.6783-0.0438-0.1680.0994-0.0265-0.08790.0626-0.15620.09560.1317-0.1742-0.011-0.0113-0.0757-0.0126-0.009856.50931.26726.778
21.3654-0.17230.28514.1546-0.60321.60070.00320.1217-0.1093-0.0231-0.0035-0.10610.05750.01240.0004-0.08140.0146-0.0355-0.1243-0.0124-0.083842.26815.78113.805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 398
2X-RAY DIFFRACTION2A399 - 590

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