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- PDB-29rx: Crystal structure of JAK2 JH1 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 29rx
TitleCrystal structure of JAK2 JH1 in complex with ADP
ComponentsTyrosine-protein kinase JAK2
KeywordsTRANSFERASE / Janus kinase / JAK2 / JH1
Function / homology
Function and homology information


nuclear receptor-mediated mineralocorticoid signaling pathway / response to interleukin-12 / histone H3Y41 kinase activity / mammary gland epithelium development / symbiont-induced defense-related programmed cell death / positive regulation of growth hormone receptor signaling pathway / interleukin-35-mediated signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / granulocyte macrophage colony-stimulating factor receptor complex / regulation of postsynapse to nucleus signaling pathway ...nuclear receptor-mediated mineralocorticoid signaling pathway / response to interleukin-12 / histone H3Y41 kinase activity / mammary gland epithelium development / symbiont-induced defense-related programmed cell death / positive regulation of growth hormone receptor signaling pathway / interleukin-35-mediated signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / granulocyte macrophage colony-stimulating factor receptor complex / regulation of postsynapse to nucleus signaling pathway / granulocyte-macrophage colony-stimulating factor signaling pathway / thrombopoietin-mediated signaling pathway / interleukin-12 receptor complex / Signaling by Erythropoietin / interleukin-23 receptor complex / Erythropoietin activates STAT5 / collagen-activated signaling pathway / interleukin-12 receptor binding / activation of Janus kinase activity / Erythropoietin activates Phospholipase C gamma (PLCG) / post-embryonic hemopoiesis / positive regulation of NK T cell proliferation / type 1 angiotensin receptor binding / positive regulation of T-helper 17 type immune response / positive regulation of MHC class II biosynthetic process / erythropoietin-mediated signaling pathway / Interleukin-23 signaling / positive regulation of cell-substrate adhesion / interleukin-12-mediated signaling pathway / positive regulation of leukocyte proliferation / positive regulation of platelet activation / positive regulation of natural killer cell proliferation / interleukin-23-mediated signaling pathway / intrinsic apoptotic signaling pathway in response to oxidative stress / interleukin-3-mediated signaling pathway / positive regulation of epithelial cell apoptotic process / interleukin-5-mediated signaling pathway / Interleukin-12 signaling / acetylcholine receptor binding / cellular response to interleukin-3 / positive regulation of platelet aggregation / Signaling by Leptin / IL-6-type cytokine receptor ligand interactions / Interleukin-27 signaling / Interleukin-35 Signalling / growth hormone receptor binding / axon regeneration / regulation of nitric oxide biosynthetic process / response to hydroperoxide / negative regulation of cell-cell adhesion / growth hormone receptor signaling pathway / extrinsic component of plasma membrane / regulation of receptor signaling pathway via JAK-STAT / Interleukin-20 family signaling / platelet-derived growth factor receptor signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-6 signaling / IFNG signaling activates MAPKs / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / enzyme-linked receptor protein signaling pathway / interleukin-6-mediated signaling pathway / positive regulation of tyrosine phosphorylation of STAT protein / peptide hormone receptor binding / MAPK3 (ERK1) activation / positive regulation of interleukin-17 production / MAPK1 (ERK2) activation / Prolactin receptor signaling / cellular response to dexamethasone stimulus / mesoderm development / negative regulation of cardiac muscle cell apoptotic process / signaling receptor activator activity / positive regulation of SMAD protein signal transduction / Interleukin-3, Interleukin-5 and GM-CSF signaling / growth hormone receptor signaling pathway via JAK-STAT / insulin receptor substrate binding / response to tumor necrosis factor / Interleukin receptor SHC signaling / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / Growth hormone receptor signaling / extrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / cell surface receptor signaling pathway via JAK-STAT / phosphatidylinositol 3-kinase binding / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / lipopolysaccharide-mediated signaling pathway / actin filament polymerization / positive regulation of T cell proliferation / negative regulation of cytokine production involved in inflammatory response / negative regulation of protein localization to chromatin / post-translational protein modification / SH2 domain binding / positive regulation of apoptotic signaling pathway / erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / endosome lumen / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of receptor signaling pathway via JAK-STAT
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 / : ...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 / SH2 domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / Tyrosine-protein kinase JAK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMiao, Y. / Haikarainen, T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland Finland
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Janus kinase 2 activation loop as a regulator of catalysis and trans-activation.
Authors: Miao, Y. / Mykuliak, V.V. / Hubbard, S.R. / Silvennoinen, O. / Hytonen, V. / Haikarainen, T.
History
DepositionApr 2, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,18210
Polymers111,8053
Non-polymers1,3787
Water9,314517
1
A: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7203
Polymers37,2681
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7203
Polymers37,2681
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein kinase JAK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7434
Polymers37,2681
Non-polymers4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.261, 69.191, 320.488
Angle α, β, γ (deg.)90.000, 90.212, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1481-

HOH

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Components

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


Mass: 37268.285 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O60674, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 0.1 M GLY-GLY PH 8.2, 1.6 M NA-MALONATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→80.12 Å / Num. obs: 101845 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.8
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4986 / CC1/2: 0.908

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→80.12 Å / SU ML: 0.2266 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 47.1271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3496 4901 4.84 %
Rwork0.3069 96334 -
obs0.309 101235 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→80.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 85 517 7994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167673
X-RAY DIFFRACTIONf_angle_d1.236610383
X-RAY DIFFRACTIONf_chiral_restr0.07671090
X-RAY DIFFRACTIONf_plane_restr0.01321334
X-RAY DIFFRACTIONf_dihedral_angle_d14.47162929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.3361500.32153252X-RAY DIFFRACTION99.79
1.82-1.840.35031650.30523145X-RAY DIFFRACTION99.64
1.84-1.860.33511550.29653300X-RAY DIFFRACTION99.6
1.86-1.890.34961700.28473113X-RAY DIFFRACTION99.64
1.89-1.910.28741680.28353188X-RAY DIFFRACTION99.7
1.91-1.940.31761890.2743244X-RAY DIFFRACTION99.65
1.94-1.970.31241730.26783138X-RAY DIFFRACTION99.64
1.97-20.34291600.27143234X-RAY DIFFRACTION99.74
2-2.030.32431600.27223254X-RAY DIFFRACTION99.62
2.03-2.060.33471310.27633153X-RAY DIFFRACTION99.64
2.06-2.10.31611700.28353309X-RAY DIFFRACTION99.43
2.1-2.130.27581550.2613142X-RAY DIFFRACTION99.49
2.13-2.180.28151950.26173210X-RAY DIFFRACTION99.68
2.18-2.220.30051710.25883168X-RAY DIFFRACTION99.52
2.22-2.270.36151850.26383199X-RAY DIFFRACTION99.47
2.27-2.320.29241710.27143194X-RAY DIFFRACTION99.53
2.32-2.380.31961660.26953250X-RAY DIFFRACTION99.5
2.38-2.440.40891450.28083201X-RAY DIFFRACTION99.52
2.44-2.510.33311480.29643270X-RAY DIFFRACTION99.62
2.51-2.60.37651500.28793204X-RAY DIFFRACTION99.67
2.6-2.690.3071790.29423198X-RAY DIFFRACTION99.68
2.69-2.80.3771630.30323246X-RAY DIFFRACTION99.56
2.8-2.920.38661490.32373221X-RAY DIFFRACTION99.59
2.92-3.080.38871740.31783200X-RAY DIFFRACTION99.32
3.08-3.270.38731830.32543218X-RAY DIFFRACTION99.24
3.27-3.520.35051600.32133218X-RAY DIFFRACTION99.09
3.52-3.880.36261750.32373243X-RAY DIFFRACTION98.67
3.88-4.440.35271430.32913192X-RAY DIFFRACTION98.44
4.44-5.590.4031600.34323275X-RAY DIFFRACTION98.62
5.59-80.120.38421380.39973155X-RAY DIFFRACTION93.26
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)
11.6494060450.849225074870.5632728435820.4499612457221.032809456861.08830218646-0.282768836380.0847942031538-0.4567035362610.1180735475490.169027705441-0.189509216322-0.8605221965130.3652422010960.01178912117350.367960400846-0.0188030989869-0.04726852443310.146039500815-0.02809821087550.0985456282058-26.7300639483-26.5686497331-13.3343383882
20.51819732299-0.8845792071660.9043117666261.212765091-1.047323088620.582949747846-0.02142571844440.08840104110730.09798305800340.175670165242-0.0453793975969-0.0103183085067-0.0720193416521-0.04623392441940.06792269664610.319152721150.01478459371590.0367895985930.179400024579-0.07167510448880.106441328257-8.28901433542-11.2832897255-21.5087490134
31.544545232432.147957436760.7979231135310.9916069926040.4816945134770.9323828783810.0516886627199-0.3496626972120.0212054391498-0.11329832284-0.14750224659-0.006974169133360.205401956673-0.2473460967350.07949850879850.1053157506330.0625230031375-0.0005865669470140.2435556645270.00744739485530.162718709631-34.8084719852-61.1876291136-66.6781930027
41.417472885310.145625073956-0.7553819385581.55352202596-1.44932666360.3131695018230.114152024797-0.408129697927-0.611205190178-0.05572641248960.0143346233405-0.151711903675-0.05455224224590.0860405801277-0.02554302187880.0876871248395-0.00632021627065-0.01691590242390.2104116825870.02815705853550.0929792505514-16.4171124128-45.9357852595-74.9678924547
51.55054947485-0.3020027336390.4551960089891.43545243502-0.02198300794030.919294265189-0.05991661576160.1130938410570.195339698289-9.0634377261E-50.0134926111868-0.4584503990220.1873740518180.1108713308460.06374736050090.111841608520.007947869836660.01801555601770.124331858046-0.01232748892310.245927835875-36.4613025798-59.6906324214-39.1896549723
61.30738388331.07373144828-0.2279675853062.498997169380.1839372178980.389870396733-0.048762298307-0.1919758160130.4552491449040.03650308204220.0548122311778-0.0636782649121-0.008680133504420.1320161566760.003541090264650.1107259054060.0128618692744-0.03542625044470.149523583863-0.03914095085630.278220853513-50.5461253377-42.7707278783-30.3429879304
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 833 through 949 )AA833 - 9491 - 117
22chain 'A' and (resid 950 through 1132 )AA950 - 1132118 - 300
33chain 'B' and (resid 833 through 949 )BC833 - 9491 - 117
44chain 'B' and (resid 950 through 1132 )BC950 - 1132118 - 300
55chain 'C' and (resid 833 through 992 )CE833 - 9921 - 160
66chain 'C' and (resid 993 through 1132 )CE993 - 1132161 - 300

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