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

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Basic information

Entry
Database: PDB / ID: 8ahg
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 / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU 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 / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / cellular response to organic cyclic compound / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / regulation of cell growth / adherens junction / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / 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 / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...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-M4I / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.885 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

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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)33,5992
Polymers33,3811
Non-polymers2181
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.822, 61.822, 180.790
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-M4I / ~{N}-methyl-3-propan-2-yl-1~{H}-pyrazolo[3,4-c]pyridine-4-carboxamide


Mass: 218.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 48.94 % / 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: 1.885→58.496 Å / Num. obs: 27812 / % possible obs: 95.3 % / Redundancy: 26.4 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.018 / Rrim(I) all: 0.092 / Net I/av σ(I): 22.7 / Net I/σ(I): 22.7
Reflection shellResolution: 1.885→1.952 Å / Redundancy: 27.2 % / Rmerge(I) obs: 3.058 / Mean I/σ(I) obs: 1 / Num. unique obs: 1390 / CC1/2: 0.638 / Rpim(I) all: 0.588 / Rrim(I) all: 3.115 / % possible all: 50.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
XDSFeb 5, 2021data reduction
AimlessV0.7.7data scaling
Coot0.9.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVA

2bva


Resolution: 1.885→58.496 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.598 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2265 1387 4.987 %
Rwork0.1785 26424 -
all0.181 --
obs-27811 94.908 %
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: 38.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.051 Å2-0 Å2-0 Å2
2---0.051 Å2-0 Å2
3---0.103 Å2
Refinement stepCycle: LAST / Resolution: 1.885→58.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 16 210 2534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162268
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6373246
X-RAY DIFFRACTIONr_angle_other_deg0.5241.5515285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1835297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.1221021
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74210424
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.41210101
X-RAY DIFFRACTIONr_chiral_restr0.0780.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02447
X-RAY DIFFRACTIONr_nbd_refined0.2130.2528
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.22183
X-RAY DIFFRACTIONr_nbtor_refined0.170.21184
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2161
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.212
X-RAY DIFFRACTIONr_nbd_other0.210.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2790.210
X-RAY DIFFRACTIONr_mcbond_it3.3973.9821177
X-RAY DIFFRACTIONr_mcbond_other3.3943.9821177
X-RAY DIFFRACTIONr_mcangle_it4.1595.961471
X-RAY DIFFRACTIONr_mcangle_other4.1595.9631472
X-RAY DIFFRACTIONr_scbond_it4.2444.4341212
X-RAY DIFFRACTIONr_scbond_other4.2424.4351213
X-RAY DIFFRACTIONr_scangle_it5.926.481772
X-RAY DIFFRACTIONr_scangle_other5.9196.4811773
X-RAY DIFFRACTIONr_lrange_it7.42479.82310327
X-RAY DIFFRACTIONr_lrange_other7.38779.17810175
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
1.885-1.9340.302420.2827200.28421290.9320.93835.79150.284
1.934-1.9870.278900.25818450.25920590.9390.95393.97770.255
1.987-2.0440.278880.24918980.2519860.9450.9581000.24
2.044-2.1070.3890.23418740.23719630.940.9641000.219
2.107-2.1760.249910.20518020.20718930.9620.9721000.188
2.176-2.2520.2581150.20317270.20618420.9580.9741000.183
2.252-2.3370.234950.19416760.19617710.9620.9761000.17
2.337-2.4320.284850.216360.20417210.9550.9761000.173
2.432-2.540.22720.18615770.18716490.9710.9791000.161
2.54-2.6640.234800.20615040.20815840.9650.9731000.179
2.664-2.8080.316810.19714450.20315260.9410.9761000.174
2.808-2.9780.235580.213630.20114210.9610.9761000.177
2.978-3.1830.244680.19412840.19713520.9580.9771000.18
3.183-3.4370.208620.18612170.18612790.9750.9811000.178
3.437-3.7640.226620.1811040.18311660.9760.9831000.175
3.764-4.2060.172570.14810270.14910840.9840.9881000.148
4.206-4.8520.177560.1239070.1269630.9820.9911000.13
4.852-5.9320.196450.1547780.1568230.9790.9881000.161
5.932-8.3470.286310.176400.1746710.9540.9851000.182
8.347-58.4960.214200.1644000.1664210.9760.98199.76250.208

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