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- PDB-3lm5: Crystal Structure of human Serine/Threonine Kinase 17B (STK17B) i... -

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Basic information

Entry
Database: PDB / ID: 3lm5
TitleCrystal Structure of human Serine/Threonine Kinase 17B (STK17B) in complex with Quercetin
ComponentsSerine/threonine-protein kinase 17B
KeywordsTRANSFERASE / STK17B / serine/threonine kinase 17B / DRAK2 / DAP kinase related apoptosis-inducing protein kinase 2 / death-associated protein kinase-related 2 / Structural Genomics / Structural Genomics Consortium / SGC / Apoptosis / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / 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 ...positive regulation of fibroblast apoptotic process / Flemming body / endoplasmic reticulum-Golgi intermediate compartment / actin cytoskeleton / protein autophosphorylation / 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 phosphorylation / positive regulation of apoptotic process / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 ...Serine/threonine-protein kinase 17B, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3,5,7,3',4'-PENTAHYDROXYFLAVONE / Serine/threonine-protein kinase 17B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsUgochukwu, E. / Soundararajan, M. / Rellos, P. / Fedorov, O. / Phillips, C. / Wang, J. / Hapka, E. / Filippakopoulos, P. / Chaikuad, A. / Pike, A.C.W. ...Ugochukwu, E. / Soundararajan, M. / Rellos, P. / Fedorov, O. / Phillips, C. / Wang, J. / Hapka, E. / Filippakopoulos, P. / Chaikuad, A. / Pike, A.C.W. / Carpenter, L. / Vollmar, M. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / 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
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 13, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_ref_seq_dif / struct_site
Item: _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id ..._struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,6292
Polymers37,3271
Non-polymers3021
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.380, 83.380, 115.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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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 / Fragment: STK17B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DRAK2, STK17B / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2
References: UniProt: O94768, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M NaCl; 0.1M BIS-TRIS pH 5.5; 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: MAR225 / Detector: CCD / Date: Dec 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.29→52.49 Å / Num. obs: 18152 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 12.5
Reflection shellResolution: 2.29→2.39 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.902 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.902 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EHA

3eha


Resolution: 2.29→52.49 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.051 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28081 894 5.1 %RANDOM
Rwork0.20011 ---
obs0.20401 16601 91.69 %-
all-16601 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.29→52.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 22 118 2325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222258
X-RAY DIFFRACTIONr_bond_other_d0.0010.021488
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9713068
X-RAY DIFFRACTIONr_angle_other_deg0.87533640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1725106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06415389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6891510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.64151368
X-RAY DIFFRACTIONr_mcbond_other2.2825550
X-RAY DIFFRACTIONr_mcangle_it7.13372219
X-RAY DIFFRACTIONr_scbond_it9.7549890
X-RAY DIFFRACTIONr_scangle_it10.46611848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.285→2.345 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 85 -
Rwork0.265 1258 -
obs--98.68 %
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)
14.57270.7863-0.65514.35780.98472.7887-0.06420.1465-0.0489-0.01310.09270.13170.19890.0018-0.02850.07820.0129-0.04880.075-0.01390.038429.9586-4.6301-3.3583
20.7583-1.6244-1.0573.50752.17681.9701-0.07230.0111-0.08980.20470.02150.18740.056-0.18220.05080.09620.0026-0.01890.13250.00670.067524.08238.07348.3119
33.8728-0.06590.09072.43470.45164.31290.08920.2190.102-0.15190.0458-0.1334-0.09450.1376-0.13510.05340.030.01960.0662-0.03950.087118.075324.78516.2447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 79
2X-RAY DIFFRACTION2A80 - 183
3X-RAY DIFFRACTION3A184 - 301

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