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- PDB-6myn: Crystal structure of murine NF-kappaB inducing kinase (NIK) bound... -

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Basic information

Entry
Database: PDB / ID: 6myn
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) bound to inhibitor R7
ComponentsMitogen-activated protein kinase kinase kinase 14
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / NIK / kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center ...CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-K6Y / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.744 Å
AuthorsHarris, S.F. / Smith, M. / Barker, J.
Citation
Journal: Acs Med.Chem.Lett. / Year: 2019
Title: Structure Based Design of Potent Selective Inhibitors of Protein Kinase D1 (PKD1).
Authors: Feng, J.A. / Lee, P. / Alaoui, M.H. / Barrett, K. / Castanedo, G. / Godemann, R. / McEwan, P. / Wang, X. / Wu, P. / Zhang, Y. / Harris, S.F. / Staben, S.T.
#1: Journal: Acs Med.Chem.Lett. / Year: 2019
Title: Structure based design of potent selective inhibitors of protein kinase D1 (PKD1)
Authors: Feng, J.W. / Lee, P. / Alaoui, M.H. / Barrett, K. / Castaneda, G.M. / Godemann, R. / McEwan, P. / Wang, X. / Wu, P. / Zhang, Y. / Harris, S.F. / Staben, S.T.
History
DepositionNov 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation_author
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 14
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2069
Polymers76,7992
Non-polymers1,4077
Water1,892105
1
A: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0554
Polymers38,3991
Non-polymers6563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1515
Polymers38,3991
Non-polymers7524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.220, 143.220, 46.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 14 / NF-kappa-beta-inducing kinase / Serine/threonine-protein kinase NIK


Mass: 38399.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, Nik / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K6Y / (5s,7s)-9-fluoro-10-[(3R)-3-hydroxy-3-(5-methyl-1,2-oxazol-3-yl)but-1-yn-1-yl]-N~3~-methyl-6,7-dihydro-5H-5,7-methanoimidazo[2,1-a][2]benzazepine-2,3-dicarboxamide


Mass: 463.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22FN5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100 mM sodium citrate tribasic dihydrate (pH 6.2), 0.5 M ammonium sulfate, 0.9 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.744→44.15 Å / Num. obs: 25142 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.27 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.106 / Rsym value: 0.086 / Net I/av σ(I): 8.4 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.744-2.826.90.691.118280.310.8160.69100
2.82-2.896.90.6411.218320.2850.7540.641100
2.89-2.986.70.4841.616900.2210.5750.48499.8
2.98-3.076.60.3652.117050.1690.4350.36599.8
3.07-3.176.20.2912.616360.140.3510.29199.8
3.17-3.285.50.2233.416030.1170.2810.22399.7
3.28-3.46.90.1624.715300.0730.1930.162100
3.4-3.5470.1295.914920.0590.1570.12999.9
3.54-3.76.90.0977.814080.0450.1190.09799.9
3.7-3.886.90.0888.713840.0410.1080.08899.9
3.88-4.096.70.0671112720.0320.0830.06799.8
4.09-4.346.80.05612.712400.0270.070.05699.9
4.34-4.646.60.0461511720.0230.060.046100
4.64-5.016.50.04615.210760.0240.0620.04699.9
5.01-5.496.30.04814.99990.0250.0640.048100
5.49-6.145.90.04615.39010.0250.0610.04699.6
6.14-7.096.10.03818.48140.0190.0470.038100
7.09-8.686.90.02922.16880.0130.0350.029100
8.68-12.276.70.02524.85560.0120.030.025100
12.27-44.156.10.024273160.0120.0290.02498.2

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.12-2829_finalrefinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.744→42.191 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.3
RfactorNum. reflection% reflection
Rfree0.255 2603 10.36 %
Rwork0.1795 --
obs0.1871 25125 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.73 Å2 / Biso mean: 55.4264 Å2 / Biso min: 26.57 Å2
Refinement stepCycle: final / Resolution: 2.744→42.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 93 105 5251
Biso mean--63.89 51.2 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015301
X-RAY DIFFRACTIONf_angle_d1.1287190
X-RAY DIFFRACTIONf_chiral_restr0.057764
X-RAY DIFFRACTIONf_plane_restr0.007976
X-RAY DIFFRACTIONf_dihedral_angle_d16.5673214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7444-2.79430.35511530.290211451298
2.7943-2.8480.38531400.277611701310
2.848-2.90610.36431410.284811771318
2.9061-2.96930.36631640.273111201284
2.9693-3.03840.36511200.230911811301
3.0384-3.11430.33941300.227712071337
3.1143-3.19850.27751310.218611581289
3.1985-3.29260.30361190.209411951314
3.2926-3.39880.27291450.207511651310
3.3988-3.52020.29531370.204911831320
3.5202-3.66110.26191480.175611671315
3.6611-3.82760.26311300.171611871317
3.8276-4.02930.23821300.160511701300
4.0293-4.28150.21721690.146911731342
4.2815-4.61170.20371250.132212181343
4.6117-5.07510.23591250.14211961321
5.0751-5.80790.24311190.162712251344
5.8079-7.31110.20881430.162512011344
7.3111-42.19570.19671340.165312841418

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