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- PDB-5hez: JAK2 kinase (JH1 domain) mutant P1057A in complex with TG101209 -

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Basic information

Entry
Database: PDB / ID: 5hez
TitleJAK2 kinase (JH1 domain) mutant P1057A in complex with TG101209
ComponentsTyrosine-protein kinase JAK2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / inhibitor / mutation / TYK2 / surrogate / P1104A / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


interleukin-35-mediated signaling pathway / nuclear receptor-mediated mineralocorticoid signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex ...interleukin-35-mediated signaling pathway / nuclear receptor-mediated mineralocorticoid signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / symbiont-induced defense-related programmed cell death / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / interleukin-12 receptor binding / Signaling by Erythropoietin / collagen-activated signaling pathway / Erythropoietin activates STAT5 / interleukin-5-mediated signaling pathway / response to interleukin-12 / Erythropoietin activates Phospholipase C gamma (PLCG) / positive regulation of leukocyte proliferation / post-embryonic hemopoiesis / interleukin-12 receptor complex / activation of Janus kinase activity / interleukin-23 receptor complex / tyrosine phosphorylation of STAT protein / Interleukin-23 signaling / positive regulation of MHC class II biosynthetic process / positive regulation of platelet aggregation / positive regulation of T-helper 17 type immune response / type 1 angiotensin receptor binding / positive regulation of platelet activation / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / acetylcholine receptor binding / cellular response to interleukin-3 / interleukin-3-mediated signaling pathway / Signaling by Leptin / regulation of nitric oxide biosynthetic process / positive regulation of signaling receptor activity / Interleukin-12 signaling / Interleukin-35 Signalling / Interleukin-27 signaling / IL-6-type cytokine receptor ligand interactions / positive regulation of epithelial cell apoptotic process / positive regulation of natural killer cell proliferation / response to hydroperoxide / positive regulation of cell-substrate adhesion / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / axon regeneration / growth hormone receptor signaling pathway / peptide hormone receptor binding / negative regulation of cardiac muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / IFNG signaling activates MAPKs / extrinsic component of plasma membrane / Interleukin-20 family signaling / interleukin-6-mediated signaling pathway / negative regulation of cell-cell adhesion / Interleukin-6 signaling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / enzyme-linked receptor protein signaling pathway / Prolactin receptor signaling / MAPK3 (ERK1) activation / positive regulation of interleukin-17 production / response to amine / negative regulation of DNA binding / positive regulation of nitric-oxide synthase biosynthetic process / MAPK1 (ERK2) activation / cell surface receptor signaling pathway via JAK-STAT / mesoderm development / positive regulation of SMAD protein signal transduction / platelet-derived growth factor receptor signaling pathway / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / growth hormone receptor signaling pathway via JAK-STAT / response to tumor necrosis factor / Interleukin receptor SHC signaling / phosphatidylinositol 3-kinase binding / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / Erythropoietin activates RAS / Growth hormone receptor signaling / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway / Signaling by CSF3 (G-CSF) / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of vascular associated smooth muscle cell proliferation / tumor necrosis factor-mediated signaling pathway / actin filament polymerization / SH2 domain binding / cellular response to dexamethasone stimulus / erythrocyte differentiation / post-translational protein modification / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of interleukin-1 beta production / caveola / endosome lumen / positive regulation of cell differentiation / positive regulation of apoptotic signaling pathway
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain ...Tyrosine-protein kinase, non-receptor Jak2 / Janus kinase 2, pseudokinase domain / Janus kinase 2, catalytic domain / Tyrosine-protein kinase JAK2, SH2 domain / JAK2, FERM domain C-lobe / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-1M3 / Tyrosine-protein kinase JAK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsUltsch, M. / Eigenbrot, C.
CitationJournal: Sci Transl Med / Year: 2016
Title: Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity.
Authors: Dendrou, C.A. / Cortes, A. / Shipman, L. / Evans, H.G. / Attfield, K.E. / Jostins, L. / Barber, T. / Kaur, G. / Kuttikkatte, S.B. / Leach, O.A. / Desel, C. / Faergeman, S.L. / Cheeseman, J. ...Authors: Dendrou, C.A. / Cortes, A. / Shipman, L. / Evans, H.G. / Attfield, K.E. / Jostins, L. / Barber, T. / Kaur, G. / Kuttikkatte, S.B. / Leach, O.A. / Desel, C. / Faergeman, S.L. / Cheeseman, J. / Neville, M.J. / Sawcer, S. / Compston, A. / Johnson, A.R. / Everett, C. / Bell, J.I. / Karpe, F. / Ultsch, M. / Eigenbrot, C. / McVean, G. / Fugger, L.
History
DepositionJan 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Derived calculations
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK2
B: Tyrosine-protein kinase JAK2
C: Tyrosine-protein kinase JAK2
D: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,15517
Polymers141,8414
Non-polymers4,31513
Water1,982110
1
A: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5805
Polymers35,4601
Non-polymers1,1204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5805
Polymers35,4601
Non-polymers1,1204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4803
Polymers35,4601
Non-polymers1,0192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5154
Polymers35,4601
Non-polymers1,0553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Tyrosine-protein kinase JAK2
B: Tyrosine-protein kinase JAK2
C: Tyrosine-protein kinase JAK2
D: Tyrosine-protein kinase JAK2
hetero molecules

A: Tyrosine-protein kinase JAK2
B: Tyrosine-protein kinase JAK2
C: Tyrosine-protein kinase JAK2
D: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,31134
Polymers283,6828
Non-polymers8,62926
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area27000 Å2
ΔGint-261 kcal/mol
Surface area96990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)211.813, 215.649, 91.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11C-1317-

HOH

21D-1309-

HOH

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Components

#1: Protein
Tyrosine-protein kinase JAK2 / Janus kinase 2 / JAK-2


Mass: 35460.219 Da / Num. of mol.: 4 / Mutation: P1057A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O60674, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-1M3 / N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide


Mass: 509.667 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C26H35N7O2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.9 M sodium malonate, 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2014
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.66→27 Å / Num. obs: 60222 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 67.8 Å2 / Rsym value: 0.151 / Net I/σ(I): 7.9
Reflection shellResolution: 2.66→2.755 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JI9

4ji9


Resolution: 2.66→26.81 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.9105 / SU R Cruickshank DPI: 0.407 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.253 / SU Rfree Cruickshank DPI: 0.259
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 2987 4.96 %RANDOM
Rwork0.2169 ---
obs0.2179 60222 99.64 %-
Displacement parametersBiso mean: 67.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.8263 Å20 Å20 Å2
2---3.6018 Å20 Å2
3---2.7756 Å2
Refine analyzeLuzzati coordinate error obs: 0.412 Å
Refinement stepCycle: 1 / Resolution: 2.66→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9493 0 293 110 9896
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910136HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.113690HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3640SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes284HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1408HARMONIC5
X-RAY DIFFRACTIONt_it10136HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion21.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1195SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11185SEMIHARMONIC4
LS refinement shellResolution: 2.66→2.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3104 214 4.98 %
Rwork0.2539 4082 -
all0.2565 4296 -
obs--99.64 %
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)
12.17121.1681-0.60220.0211-0.80962.28360.0555-0.0549-0.10430.1654-0.0224-0.06560.2359-0.0265-0.0331-0.0085-0.0152-0.0854-0.1389-0.04310.0919-33.8088-64.327333.4886
24.05110.84240.04292.15070.12791.75910.0236-0.0157-0.03410.1061-0.14520.1710.1614-0.01430.1217-0.11370.0506-0.0613-0.0879-0.0177-0.0793-18.5494-55.63936.4058
31.5138-0.13650.6710.9916-0.78232.02730.01160.0490.2731-0.06620.0287-0.1793-0.4047-0.0932-0.0403-0.07740.0327-0.0236-0.0106-0.0003-0.017-10.344-41.220733.9487
42.02180.79790.02070.94120.33942.22940.013-0.0721-0.1585-0.00070.0805-0.16250.05470.2584-0.0935-0.08830.03850.0004-0.1356-0.02630.1391-42.1359-33.852734.9808
52.3915-0.93980.11793.7198-0.54271.42450.0479-0.054-0.2821-0.0138-0.08820.0803-0.15480.1470.0403-0.0845-0.02260.0093-0.163-0.069-0.043-50.8268-18.85137.0044
61.19720.81660.65231.04-0.0852.03560.040.08150.2033-0.0212-0.00910.19660.0707-0.2899-0.0310.0270.0205-0.0239-0.0784-0.07250.0015-65.7407-10.670434.1476
72.368-0.5550.54590.09450.03382.34360.00940.04250.11050.09370.0181-0.0244-0.1526-0.2341-0.0275-0.08060.0180.0217-0.1019-0.01790.1039-44.002-34.03633.9405
83.60380.05590.23422.97780.02282.4717-0.05470.1840.1157-0.1205-0.07910.028-0.198-0.0170.1338-0.1424-0.02460.0308-0.18490.0293-0.033-26.9269-31.86281.0111
93.6602-0.4670.85412.363-0.15583.52970.0330.18880.11320.09990.085-0.13730.25050.4512-0.118-0.171-0.04710.0111-0.05490.0328-0.0754-11.456-38.65953.5989
104.54261.1611-0.72683.66161.79312.43240.013-0.0056-0.27880.0480.08560.080.2243-0.1504-0.0987-0.11510.00310.0091-0.14180.06140.0735-73.7777-44.16272.4148
113.1409-1.0604-0.39726.22591.81922.299-0.1836-0.03960.0472-0.33480.10910.1503-0.1242-0.13070.0745-0.14630.0225-0.0322-0.23690.0418-0.0864-75.8426-26.91150.5658
122.10750.00980.88054.9695-0.09384.6557-0.0009-0.10610.0559-0.4340.04430.1859-0.35990.2702-0.04350.01720.0655-0.0574-0.2947-0.0031-0.0807-68.864-11.59933.6298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|842 - A|903 }A842 - 903
2X-RAY DIFFRACTION2{ A|904 - A|1032 A|1204 - A|1204 }A904 - 1032
3X-RAY DIFFRACTION2{ A|904 - A|1032 A|1204 - A|1204 }A1204
4X-RAY DIFFRACTION3{ A|1033 - A|1132 A|1203 - A|1203 }A1033 - 1132
5X-RAY DIFFRACTION3{ A|1033 - A|1132 A|1203 - A|1203 }A1203
6X-RAY DIFFRACTION4{ B|842 - B|903 }B842 - 903
7X-RAY DIFFRACTION5{ B|904 - B|1032 B|1203 - B|1203 }B904 - 1032
8X-RAY DIFFRACTION5{ B|904 - B|1032 B|1203 - B|1203 }B1203
9X-RAY DIFFRACTION6{ B|1033 - B|1132 B|1202 - B|1202 }B1033 - 1132
10X-RAY DIFFRACTION6{ B|1033 - B|1132 B|1202 - B|1202 }B1202
11X-RAY DIFFRACTION7{ C|842 - C|903 }C842 - 903
12X-RAY DIFFRACTION8{ C|904 - C|1032 C|1201 - C|1201 }C904 - 1032
13X-RAY DIFFRACTION8{ C|904 - C|1032 C|1201 - C|1201 }C1201
14X-RAY DIFFRACTION9{ C|1033 - C|1132 C|1202 - C|1202 }C1033 - 1132
15X-RAY DIFFRACTION9{ C|1033 - C|1132 C|1202 - C|1202 }C1202
16X-RAY DIFFRACTION10{ D|842 - D|903 }D842 - 903
17X-RAY DIFFRACTION11{ D|904 - D|1032 D|1203 - D|1203 }D904 - 1032
18X-RAY DIFFRACTION11{ D|904 - D|1032 D|1203 - D|1203 }D1203
19X-RAY DIFFRACTION12{ D|1033 - D|1132 D|1202 - D|1202 }D1033 - 1132
20X-RAY DIFFRACTION12{ D|1033 - D|1132 D|1202 - D|1202 }D1202

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