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- PDB-4equ: Human STK-10 (LOK) kinase domain in DFG-out conformation with inh... -

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Basic information

Entry
Database: PDB / ID: 4equ
TitleHuman STK-10 (LOK) kinase domain in DFG-out conformation with inhibitor DSA-7
ComponentsSerine/threonine-protein kinase 10
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / serine/threonine kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / protein autophosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity ...lymphocyte aggregation / regulation of lymphocyte migration / RHOB GTPase cycle / RHOC GTPase cycle / RHOA GTPase cycle / specific granule membrane / 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 / intracellular signal transduction / nuclear body / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / : / Polo kinase kinase / 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. ...Serine/threonine-protein kinase 10, catalytic domain / Polo kinase kinase / : / Polo kinase kinase / 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
Chem-G6I / Serine/threonine-protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsMerritt, E.A. / Larson, E.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Affinity-Based Probes Based on Type II Kinase Inhibitors.
Authors: Ranjitkar, P. / Perera, B.G. / Swaney, D.L. / Hari, S.B. / Larson, E.T. / Krishnamurty, R. / Merritt, E.A. / Villen, J. / Maly, D.J.
History
DepositionApr 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Structure summary
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase 10
B: Serine/threonine-protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,17910
Polymers68,5972
Non-polymers1,5828
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-42 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.810, 49.040, 133.760
Angle α, β, γ (deg.)90.000, 101.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 24 - 317 / Label seq-ID: 9 - 302

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Serine/threonine-protein kinase 10 / Lymphocyte-oriented kinase


Mass: 34298.605 Da / Num. of mol.: 2 / Fragment: kinase domain (UNP residues 18-317)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STK10, LOK / Production host: Escherichia coli (E. coli)
References: UniProt: O94804, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-G6I / N-{3-[(3-{4-[(4-methoxyphenyl)amino]-1,3,5-triazin-2-yl}pyridin-2-yl)amino]-4-methylphenyl}-3-(trifluoromethyl)benzamide


Mass: 571.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H24F3N7O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 0.1 M NaCacodylate pH 6.25, 0.24 M CaAcetate, 50% PEG 300, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 26, 2011
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→60.586 Å / Num. all: 51438 / Num. obs: 51438 / % possible obs: 96.4 % / Redundancy: 4 % / Rsym value: 0.089 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.113.40.6441.22172963240.64482.5
2.11-2.244.10.4711.62944172310.47198.2
2.24-2.394.10.3472.12782167780.34798.4
2.39-2.584.10.2323.22618763560.23298.7
2.58-2.834.10.1614.52397758380.16198.8
2.83-3.164.10.1056.32181153040.10598.9
3.16-3.654.10.0747.61930246960.07499.1
3.65-4.474.10.0618.91647540270.06199.3
4.47-6.324.10.068.61261831140.0699.4
6.32-60.5863.90.03914.9692717700.03998.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MIR / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2503 / WRfactor Rwork: 0.2291 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8166 / SU B: 9.881 / SU ML: 0.132 / SU R Cruickshank DPI: 0.176 / SU Rfree: 0.1544 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 2620 5.1 %RANDOM
Rwork0.223 ---
obs0.2242 51394 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 137.35 Å2 / Biso mean: 57.0501 Å2 / Biso min: 24.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å21.7 Å2
2---2.09 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4301 0 105 81 4487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024512
X-RAY DIFFRACTIONr_bond_other_d0.0030.023000
X-RAY DIFFRACTIONr_angle_refined_deg1.3932.0026131
X-RAY DIFFRACTIONr_angle_other_deg1.033.0027318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5825551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01524.438178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5891522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214931
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02833
Refine LS restraints NCS

Ens-ID: 1 / Number: 9608 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.07 / Type: LOCAL / Weight: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 143 -
Rwork0.314 2730 -
all-2873 -
obs--75.17 %
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)
17.7637-3.6233-0.02656.5748-1.81994.6865-0.0769-0.56270.25520.73760.0145-0.6561-0.34231.11490.06250.1497-0.028-0.12820.4563-0.09920.371479.87715.3316.9025
22.0519-0.2264-0.84982.19670.14632.4429-0.0175-0.1488-0.06210.11320.0098-0.44750.13590.46690.00770.33530.0230.03250.14980.00130.169763.083312.234312.0294
32.85991.5349-0.25341.0573-0.24370.0734-0.19220.2140.0416-0.45650.1547-0.1030.1804-0.04910.03740.5867-0.00040.13550.28730.03650.332650.5806-5.720531.1735
41.08780.2702-0.60211.6049-0.53722.41660.00620.0941-0.0133-0.04350.00240.1680.0913-0.2795-0.00860.2815-0.00260.02090.13390.00810.142646.206214.203712.8223
59.51914.1917-1.188610.0687-3.3696.3598-0.1534-0.1009-0.1252-0.2808-0.2479-0.36530.56541.26780.40130.07050.0951-0.04580.5701-0.03130.477771.9794-16.241156.6061
61.70930.08050.04791.33370.09952.12490.0236-0.05540.0948-0.0786-0.0004-0.3239-0.07270.3653-0.02320.052-0.0119-0.0480.298-0.00590.287656.5375-12.270254.6837
72.6585-0.50331.46711.3765-1.74022.48430.1546-0.3132-0.15120.1767-0.05130.0302-0.1972-0.0403-0.10340.563-0.03290.07980.20410.03630.163750.28235.7733.2382
80.6545-0.1992-0.122.0292-0.36011.83480.028-0.00050.0287-0.2204-0.00680.0991-0.0392-0.2279-0.02110.0741-0.0032-0.05790.26130.00230.237939.0618-14.331647.916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 78
2X-RAY DIFFRACTION2A79 - 176
3X-RAY DIFFRACTION3A177 - 213
4X-RAY DIFFRACTION4A214 - 317
5X-RAY DIFFRACTION5B24 - 55
6X-RAY DIFFRACTION6B56 - 176
7X-RAY DIFFRACTION7B177 - 214
8X-RAY DIFFRACTION8B215 - 317

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