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- PDB-8ahh: PAC FragmentDEL: Photoactivated covalent capture of DNA encoded f... -

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Basic information

Entry
Database: PDB / ID: 8ahh
TitlePAC FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE / PROTEIN KINASE / PAK4 / ATP-BINDING / TECHNOLOGY
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 / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / RAC1 GTPase cycle / cytoskeleton organization / cellular response to starvation / adherens junction / regulation of cell growth / positive regulation of angiogenesis / cell migration / 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 / cytoplasm / cytosol
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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
Similarity search - Domain/homology
Chem-M4X / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.037 Å
AuthorsBaker, L.M. / Murray, J.B. / Hubbard, R.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Med Chem / Year: 2022
Title: PAC-FragmentDEL - photoactivated covalent capture of DNA-encoded fragments for hit discovery.
Authors: Ma, H. / Murray, J.B. / Luo, H. / Cheng, X. / Chen, Q. / Song, C. / Duan, C. / Tan, P. / Zhang, L. / Liu, J. / Morgan, B.A. / Li, J. / Wan, J. / Baker, L.M. / Finnie, W. / Guetzoyan, L. / ...Authors: Ma, H. / Murray, J.B. / Luo, H. / Cheng, X. / Chen, Q. / Song, C. / Duan, C. / Tan, P. / Zhang, L. / Liu, J. / Morgan, B.A. / Li, J. / Wan, J. / Baker, L.M. / Finnie, W. / Guetzoyan, L. / Harris, R. / Hendrickson, N. / Matassova, N. / Simmonite, H. / Smith, J. / Hubbard, R.E. / Liu, G.
History
DepositionJul 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5812
Polymers33,3811
Non-polymers2001
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.897, 61.897, 180.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 33380.742 Da / Num. of mol.: 1 / Mutation: L310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-M4X / 5-cyano-~{N}-methyl-pyrazolo[1,5-a]pyridine-3-carboxamide


Mass: 200.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.49 Å3/Da / Density % sol: 50.18 % / Description: Prisms
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.8M Na/K tartrate 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 19, 2021
RadiationMonochromator: Laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.037→58.589 Å / Num. obs: 20091 / % possible obs: 94.6 % / Redundancy: 26 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.019 / Rrim(I) all: 0.099 / Net I/σ(I): 21.4
Reflection shellResolution: 2.037→2.173 Å / Redundancy: 26.3 % / Rmerge(I) obs: 2.747 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1005 / CC1/2: 0.699 / Rpim(I) all: 0.542 / Rrim(I) all: 2.801 / % possible all: 52.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSFe5 5, 2021data reduction
AimlessV0.7.7data scaling
Coot0.9.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVA

2bva


Resolution: 2.037→58.539 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.665 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.209 / ESU R Free: 0.196
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2501 1017 5.062 %
Rwork0.1842 19074 -
all0.188 --
obs-20091 86.065 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.888 Å2
Baniso -1Baniso -2Baniso -3
1--0.102 Å2-0 Å20 Å2
2---0.102 Å20 Å2
3---0.204 Å2
Refinement stepCycle: LAST / Resolution: 2.037→58.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 15 147 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162248
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.6373228
X-RAY DIFFRACTIONr_angle_other_deg0.5071.5515238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.3681022
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33810423
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.44710102
X-RAY DIFFRACTIONr_chiral_restr0.070.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
X-RAY DIFFRACTIONr_nbd_refined0.2080.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22162
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21191
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2117
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.211
X-RAY DIFFRACTIONr_nbd_other0.1850.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3540.27
X-RAY DIFFRACTIONr_mcbond_it4.5535.0321173
X-RAY DIFFRACTIONr_mcbond_other4.555.0321173
X-RAY DIFFRACTIONr_mcangle_it5.77.5381465
X-RAY DIFFRACTIONr_mcangle_other5.6997.5421466
X-RAY DIFFRACTIONr_scbond_it5.6745.4841207
X-RAY DIFFRACTIONr_scbond_other5.6725.4831208
X-RAY DIFFRACTIONr_scangle_it7.5448.051762
X-RAY DIFFRACTIONr_scangle_other7.5428.051763
X-RAY DIFFRACTIONr_lrange_it9.542101.49611418
X-RAY DIFFRACTIONr_lrange_other9.549101.20711341
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.037-2.0890.27340.2841070.28416840.9410.9436.59140.289
2.089-2.1470.295290.274780.27116370.9340.94830.97130.271
2.147-2.2090.27520.2510560.25116080.9350.95368.90550.244
2.209-2.2770.305700.25114320.25315510.9250.95296.84070.244
2.277-2.3510.376730.25314220.25914950.9240.9551000.237
2.351-2.4330.32760.24713980.25114740.9280.9591000.229
2.433-2.5250.352700.22813300.23514000.9280.9651000.206
2.525-2.6280.301650.22113070.22513720.9460.9711000.194
2.628-2.7450.269660.2112440.21313100.9680.9741000.181
2.745-2.8780.278650.22111920.22412570.950.971000.194
2.878-3.0340.27660.22411490.22712150.9540.9691000.199
3.034-3.2170.273580.21410840.21711420.9540.9711000.193
3.217-3.4380.277540.20210360.20510900.9480.9751000.19
3.438-3.7130.281430.1939560.1979990.9520.9781000.186
3.713-4.0660.211390.179060.1719450.9730.9831000.165
4.066-4.5430.181450.138110.1338560.9820.991000.132
4.543-5.240.184420.1287210.1317640.9810.9999.86910.133
5.24-6.4050.308440.1646220.1726660.9590.9861000.168
6.405-9.0050.207330.1525060.1555390.9840.9881000.166
9.005-58.5390.21230.173160.1733390.9620.981000.207

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