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- PDB-9j4p: Regulatory domain and kinase domain of ALPK1 protein -

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Basic information

Entry
Database: PDB / ID: 9j4p
TitleRegulatory domain and kinase domain of ALPK1 protein
Components(Alpha-protein kinase 1) x 2
KeywordsANTIVIRAL PROTEIN / Complex / Kinase / Immunity
Function / homology
Function and homology information


Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / photoreceptor connecting cilium / monosaccharide binding / cytoplasmic pattern recognition receptor signaling pathway / cilium assembly / Alpha-protein kinase 1 signaling pathway / response to bacterium / TAK1-dependent IKK and NF-kappa-B activation / spindle pole ...Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / photoreceptor connecting cilium / monosaccharide binding / cytoplasmic pattern recognition receptor signaling pathway / cilium assembly / Alpha-protein kinase 1 signaling pathway / response to bacterium / TAK1-dependent IKK and NF-kappa-B activation / spindle pole / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / ciliary basal body / cilium / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / cytosol
Similarity search - Function
Alpha-protein kinase 1 / MHCK/EF2 kinase / Alpha-kinase family / Alpha-type protein kinase domain profile. / Alpha-kinase family / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Alpha-protein kinase 1 / Alpha-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsXu, C. / Xu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Regulatory domain and kinase domain of ALPK1 protein
Authors: Xu, C. / Xu, T.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Alpha-protein kinase 1
A: Alpha-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3834
Polymers81,6982
Non-polymers6852
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-16 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.383, 93.383, 172.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Alpha-protein kinase 1 / Chromosome 4 kinase / Lymphocyte alpha-protein kinase


Mass: 49545.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALPK1, KIAA1527, LAK / Production host: Escherichia coli (E. coli)
References: UniProt: Q96QP1, non-specific serine/threonine protein kinase
#2: Protein Alpha-protein kinase 1


Mass: 32152.516 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Alpk1, Kiaa1527 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9CXB8, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-DY0 / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 619.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N5O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 12% PEG3350 and 0.1 M CBTP, pH 8.2, 0.1% seed

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→46.82 Å / Num. obs: 35402 / % possible obs: 99 % / Redundancy: 2.3 % / Biso Wilson estimate: 31.03 Å2 / CC1/2: 1 / Net I/σ(I): 1.64
Reflection shellResolution: 2.25→2.31 Å / Num. unique obs: 1172 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
HKL-20002.7data reduction
PHASER1.3phasing
BUCCANEER0.1model building
PHENIX1.13refinement
HKL-20002.7data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→38.01 Å / SU ML: 0.2312 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1779 5.03 %
Rwork0.2062 33610 -
obs0.2077 35389 84.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.23 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5434 0 41 222 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00795579
X-RAY DIFFRACTIONf_angle_d0.98297551
X-RAY DIFFRACTIONf_chiral_restr0.053862
X-RAY DIFFRACTIONf_plane_restr0.0083954
X-RAY DIFFRACTIONf_dihedral_angle_d18.70322068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.2868590.2911172X-RAY DIFFRACTION38.6
2.31-2.380.3002870.24561633X-RAY DIFFRACTION54.11
2.38-2.450.2905950.25151922X-RAY DIFFRACTION63.07
2.45-2.540.3003880.25072149X-RAY DIFFRACTION70.61
2.54-2.640.26541170.24862450X-RAY DIFFRACTION80.42
2.64-2.760.28481500.25252727X-RAY DIFFRACTION89.65
2.76-2.910.24661670.25162969X-RAY DIFFRACTION97.54
2.91-3.090.28451360.24033059X-RAY DIFFRACTION99.91
3.09-3.330.24761570.2283088X-RAY DIFFRACTION99.88
3.33-3.670.24221660.1983052X-RAY DIFFRACTION99.78
3.67-4.20.21971710.17653072X-RAY DIFFRACTION99.27
4.2-5.280.18761800.16253114X-RAY DIFFRACTION99.91
5.29-38.010.21192060.1823203X-RAY DIFFRACTION98.96
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)
10.6949056491990.298364656294-0.2628474244561.367379581040.06332141518470.5617216538020.0562908505438-0.2799130232260.06501494870630.1965143669070.0195356554332-0.0824692404118-0.06601013418530.1140234140630.2911652923380.1786000216320.07556355683620.006472595091920.3593138510180.02764126029750.18049603544136.962951946143.147331953652.9149912686
20.5840450554460.0175834493664-0.02439009795380.1626098483810.5530440456481.169688814610.074267023182-0.716901457453-0.3276690379310.08582318576470.169870436846-1.11370256503-0.2657987331650.0817831115148-0.5344490154340.266207496430.178275050104-0.2098426034370.4918498803960.412658397314-0.66537705820128.454597553128.283229176161.5574131916
30.2889387697280.220845292180.08124738766340.36043017179-0.2550751378230.220182469344-0.1392188607620.0508133973693-0.3505469513630.004330937209470.07470069784520.180637445616-0.0019039126481-0.1978186975120.6558453445620.185534058910.01257073294440.0283671243080.385669429808-0.03697881928230.3327722307856.1471883926623.22457796632.7200662384
40.470972173291-0.166654832256-0.1691104970440.544458701602-0.0987096927560.436371441343-0.09042443631190.02381782845190.17290217088-0.01306789238260.06141245518690.00291731382129-0.347125651842-0.0971979373220.07881101438120.2912984010180.08628487579390.01023683991110.3646688078530.011889615720.339915683212.085667512836.552029047940.6747983951
50.788242908206-0.0446890682194-0.2915433395160.565647200723-0.43364821420.802402318193-0.06993071943050.0353268638514-0.107829135677-0.01997770066990.06095873089610.06897728627060.155565552584-0.0274311846569-0.8565817344030.233875286172-0.00569857316459-0.004488570629630.3464909868590.04984755418590.30071010413720.53071870140.850247883530.5458516459
60.133373255173-0.02433882238710.08949016960350.207450457397-0.1264171779410.3150446837-0.0496081374976-0.1270455292130.385505489289-0.0250177420176-0.138363576029-0.057036262172-0.3068297840270.0323404955520.04451440542440.390327078957-0.0112771795356-0.06414668648240.2775359308690.001046096002980.53024033419317.302681002349.350420324936.2181784048
71.09336632822-0.0775288150871-0.02761902099571.04614419934-0.4262740719750.535927001997-0.1222257017760.3109724796710.315237812838-0.1774606456430.1151857695290.317391857985-0.0931759541942-0.0984393120327-0.09469580678830.318236653596-0.0912270770494-0.0779905692730.7435221081890.3105302339340.61635803474121.721861260451.312951921818.9834142549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 393 )BA1 - 3931 - 374
22chain 'B' and (resid 394 through 446 )BA394 - 446375 - 427
33chain 'A' and (resid 3 through 47 )AB3 - 471 - 45
44chain 'A' and (resid 48 through 113 )AB48 - 11346 - 103
55chain 'A' and (resid 114 through 162 )AB114 - 162104 - 152
66chain 'A' and (resid 163 through 192 )AB163 - 192153 - 170
77chain 'A' and (resid 193 through 277 )AB193 - 277171 - 255

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