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

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Basic information

Entry
Database: PDB / ID: 8ahi
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
~{N}-methyl-1,3-benzothiazole-6-carboxamide / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 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 20, 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)33,5732
Polymers33,3811
Non-polymers1921
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.913, 61.913, 181.903
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-M56 / ~{N}-methyl-1,3-benzothiazole-6-carboxamide


Mass: 192.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.52 Å3/Da / Density % sol: 50.72 % / 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: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54184 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.69→25.603 Å / Num. obs: 18685 / % possible obs: 99.2 % / Redundancy: 14.25 % / Rmerge(I) obs: 0.2074 / Net I/σ(I): 10.07
Reflection shellResolution: 2.69→2.73 Å / Redundancy: 14.25 % / Rmerge(I) obs: 0.5548 / Mean I/σ(I) obs: 3.45 / Num. unique obs: 435 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
SAINTV8.40Adata reduction
SADABSV2014/5data scaling
Coot0.9.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVA

2bva


Resolution: 2.69→25.603 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.652 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / ESU R Free: 0.341
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2489 515 4.947 %
Rwork0.1552 9895 -
all0.16 --
obs-10410 99.237 %
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: 29.915 Å2
Baniso -1Baniso -2Baniso -3
1--1.154 Å2-0 Å20 Å2
2---1.154 Å2-0 Å2
3---2.308 Å2
Refinement stepCycle: LAST / Resolution: 2.69→25.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 13 152 2475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122372
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162251
X-RAY DIFFRACTIONr_angle_refined_deg2.0271.643214
X-RAY DIFFRACTIONr_angle_other_deg0.6281.5525244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0415291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.489.77322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49810425
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.51910102
X-RAY DIFFRACTIONr_chiral_restr0.0850.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02447
X-RAY DIFFRACTIONr_nbd_refined0.2260.2529
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.22228
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21151
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2122
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.212
X-RAY DIFFRACTIONr_nbd_other0.1710.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3990.24
X-RAY DIFFRACTIONr_mcbond_it3.23.0231167
X-RAY DIFFRACTIONr_mcbond_other3.1913.0231167
X-RAY DIFFRACTIONr_mcangle_it4.8814.5241457
X-RAY DIFFRACTIONr_mcangle_other4.884.5281458
X-RAY DIFFRACTIONr_scbond_it4.0443.4431205
X-RAY DIFFRACTIONr_scbond_other4.0433.4431206
X-RAY DIFFRACTIONr_scangle_it5.9944.9891757
X-RAY DIFFRACTIONr_scangle_other5.9924.991758
X-RAY DIFFRACTIONr_lrange_it9.02759.1349797
X-RAY DIFFRACTIONr_lrange_other9.02359.149715
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
2.69-2.7590.255360.2276950.2287310.9520.9581000.207
2.759-2.8340.338450.2226910.2297360.9040.961000.2
2.834-2.9150.382310.216630.2186940.8980.9651000.187
2.915-3.0040.306390.1956640.2017030.9390.9681000.173
3.004-3.1010.314230.1816520.1866750.9280.9741000.163
3.101-3.2080.273370.1845920.1896330.9420.97599.36810.164
3.208-3.3270.321300.1665910.1736260.9350.97899.20130.149
3.327-3.460.225360.1625760.1666170.9560.9899.18960.146
3.46-3.6110.286300.1715510.1775860.9440.9899.14680.158
3.611-3.7840.284320.1615120.1695490.9520.98199.08930.15
3.784-3.9840.185220.165160.1615450.9750.98198.71560.15
3.984-4.2190.177280.1264730.1295110.980.98998.04310.124
4.219-4.5010.096220.1014650.1014920.9940.99398.98370.099
4.501-4.850.184260.0944260.0994540.9750.99499.55950.096
4.85-5.2930.29190.1153980.1214210.970.99199.04990.113
5.293-5.8870.297190.1383710.1453920.9770.98799.48980.132
5.887-6.7380.237100.1393480.1423600.9790.98499.44440.133
6.738-8.1140.245150.1322910.1383070.960.98699.67430.136
8.114-10.9380.211120.112430.1142560.9760.99199.60940.128
10.938-25.6030.30630.211770.2131820.9960.97198.90110.244

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