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- PDB-6zjf: Crystal structure of STK17B (DRAK2) in complex with AP-229 -

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Basic information

Entry
Database: PDB / ID: 6zjf
TitleCrystal structure of STK17B (DRAK2) in complex with AP-229
ComponentsSerine/threonine-protein kinase 17B
KeywordsTRANSFERASE / kinase inhibitor / DRAK2 / STK17B / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation ...positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane
Similarity search - Function
Serine/threonine-protein kinase 17B, catalytic domain / 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
Similarity search - Domain/homology
Chem-QM2 / Serine/threonine-protein kinase 17B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChaikuad, A. / Picado, A. / Willson, T. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2020
Title: A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.
Authors: Picado, A. / Chaikuad, A. / Wells, C.I. / Shrestha, S. / Zuercher, W.J. / Pickett, J.E. / Kwarcinski, F.E. / Sinha, P. / de Silva, C.S. / Zutshi, R. / Liu, S. / Kannan, N. / Knapp, S. / ...Authors: Picado, A. / Chaikuad, A. / Wells, C.I. / Shrestha, S. / Zuercher, W.J. / Pickett, J.E. / Kwarcinski, F.E. / Sinha, P. / de Silva, C.S. / Zutshi, R. / Liu, S. / Kannan, N. / Knapp, S. / Drewry, D.H. / Willson, T.M.
History
DepositionJun 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: 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 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 17B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7944
Polymers37,3271
Non-polymers4673
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint7 kcal/mol
Surface area15240 Å2
Unit cell
Length a, b, c (Å)83.349, 83.349, 114.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

21A-623-

HOH

31A-707-

HOH

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Components

#1: Protein Serine/threonine-protein kinase 17B / DAP kinase-related apoptosis-inducing protein kinase 2


Mass: 37327.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK17B, DRAK2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O94768, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-QM2 / 2-[6-(4-cyclopropylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid


Mass: 342.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 19% PEG 3350, 0.1M NaCl, 0.1M bis-tris 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→37.27 Å / Num. obs: 41311 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.817.40.8652.139900.5090.3610.998100
6.78-37.276.20.0388360.9980.0170.04299.3

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LM0

3lm0


Resolution: 1.75→37.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.68 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0996 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2036 4.9 %RANDOM
Rwork0.1794 ---
obs0.1809 39226 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.56 Å2 / Biso mean: 31.099 Å2 / Biso min: 15.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.75→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 35 231 2624
Biso mean--30.52 40.11 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132577
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172372
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6393503
X-RAY DIFFRACTIONr_angle_other_deg1.3811.5725536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.575323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85923.504137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.615461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3261513
X-RAY DIFFRACTIONr_chiral_restr0.0890.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02524
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 130 -
Rwork0.288 2853 -
all-2983 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 60.1676 Å / Origin y: 11.9419 Å / Origin z: -5.3187 Å
111213212223313233
T0.01 Å2-0.0035 Å2-0.0009 Å2-0.0427 Å20.0144 Å2--0.0155 Å2
L0.0865 °20.1722 °2-0.1341 °2-0.419 °2-0.2642 °2--0.2596 °2
S0.0079 Å °-0.0034 Å °0.0101 Å °0.0004 Å °0.01 Å °0.0055 Å °0.0041 Å °0.0264 Å °-0.0179 Å °

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