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- PDB-5t8q: Crystal structure of murine NF-kappaB inducing kinase (NIK) bound... -

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Basic information

Entry
Database: PDB / ID: 5t8q
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) bound to aryl pyrrole fragment 17
ComponentsMitogen-activated protein kinase kinase kinase 14
KeywordsTRANSFERASE / protein serine/threonine kinase / NF-kappaB / MAP3K14
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 / protein serine kinase activity / 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 ...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
1-[(2-chlorophenyl)methyl]pyrrole-2-carboxamide / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.63 Å
AuthorsSmith, M.A. / McEwan, P.A. / Hymowitz, S.G.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Based Design of Tricyclic NF-kappa B Inducing Kinase (NIK) Inhibitors That Have High Selectivity over Phosphoinositide-3-kinase (PI3K).
Authors: Castanedo, G.M. / Blaquiere, N. / Beresini, M. / Bravo, B. / Brightbill, H. / Chen, J. / Cui, H.F. / Eigenbrot, C. / Everett, C. / Feng, J. / Godemann, R. / Gogol, E. / Hymowitz, S. / ...Authors: Castanedo, G.M. / Blaquiere, N. / Beresini, M. / Bravo, B. / Brightbill, H. / Chen, J. / Cui, H.F. / Eigenbrot, C. / Everett, C. / Feng, J. / Godemann, R. / Gogol, E. / Hymowitz, S. / Johnson, A. / Kayagaki, N. / Kohli, P.B. / Knuppel, K. / Kraemer, J. / Kruger, S. / Loke, P. / McEwan, P. / Montalbetti, C. / Roberts, D.A. / Smith, M. / Steinbacher, S. / Sujatha-Bhaskar, S. / Takahashi, R. / Wang, X. / Wu, L.C. / Zhang, Y. / Staben, S.T.
History
DepositionSep 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3May 8, 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)78,61315
Polymers77,0872
Non-polymers1,52613
Water1,27971
1
A: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2587
Polymers38,5431
Non-polymers7156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3558
Polymers38,5431
Non-polymers8117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.969, 143.969, 46.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 38543.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, Nik / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-76Y / 1-[(2-chlorophenyl)methyl]pyrrole-2-carboxamide


Mass: 234.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11ClN2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.3-0.9M ammonium sulphate, 0.05-0.1M sodium citrate, 0.7-1.0M Lithium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.63→28.79 Å / Num. obs: 28412 / % possible obs: 98.5 % / Redundancy: 5.9 % / Rsym value: 0.074 / Net I/σ(I): 16.6
Reflection shellResolution: 2.63→2.76 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.66 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.63→28.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.781 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.31 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25024 2953 10.4 %RANDOM
Rwork0.19796 ---
obs0.20325 25565 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.944 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2---0.07 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.63→28.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5060 0 87 71 5218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195273
X-RAY DIFFRACTIONr_bond_other_d0.0020.025134
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9917138
X-RAY DIFFRACTIONr_angle_other_deg0.9993.00411723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64423.379219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.94615907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3531538
X-RAY DIFFRACTIONr_chiral_restr0.0860.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215834
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3343.5452603
X-RAY DIFFRACTIONr_mcbond_other1.3283.5432602
X-RAY DIFFRACTIONr_mcangle_it2.245.3113246
X-RAY DIFFRACTIONr_mcangle_other2.245.3133247
X-RAY DIFFRACTIONr_scbond_it1.513.7842670
X-RAY DIFFRACTIONr_scbond_other1.513.7842671
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3895.6153891
X-RAY DIFFRACTIONr_long_range_B_refined5.00228.0775678
X-RAY DIFFRACTIONr_long_range_B_other5.00128.085679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.631→2.699 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 190 -
Rwork0.308 1606 -
obs--85.04 %
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)
13.3247-0.49440.17595.5868-0.85152.9261-0.00180.0512-0.0528-0.0446-0.0530.12470.1312-0.11970.05480.0558-0.00470.05210.0883-0.06990.107428.403327.7455-0.7572
21.079-0.57980.52815.71960.04590.5248-0.0584-0.01050.0158-0.06690.0946-0.0648-0.11890.1455-0.03620.1369-0.03620.08780.1136-0.03510.075121.908444.77621.6083
33.82021.17470.88314.86330.56025.5018-0.35280.27820.2585-0.48270.15490.2251-0.2138-0.20620.1980.2095-0.02650.07190.03570.01170.186616.347662.3654-5.1852
43.552-0.5588-0.635.5754-0.1524.58270.07770.13690.0615-0.1178-0.02960.10980.0542-0.0293-0.04820.00490.0085-0.00580.0943-0.070.062640.0311-0.39965.0915
53.51971.94040.08493.7325-0.46190.88610.07360.03760.1333-0.0703-0.0436-0.1032-0.07220.3202-0.03010.07920.00260.04450.2051-0.06270.087147.881316.39275.9395
64.3313-0.2687-0.52273.7110.24446.10080.09730.03290.68920.034-0.18010.0329-0.61780.05150.08280.143-0.05460.12920.1279-0.07740.32755.188733.36361.1019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A334 - 410
2X-RAY DIFFRACTION2A411 - 543
3X-RAY DIFFRACTION3A544 - 675
4X-RAY DIFFRACTION4B334 - 410
5X-RAY DIFFRACTION5B411 - 554
6X-RAY DIFFRACTION6B555 - 674

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