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- PDB-6g4z: Crystal structure of murine NF-kappaB inducing kinase (NIK) in co... -

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Basic information

Entry
Database: PDB / ID: 6g4z
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) in complex with compound 2f
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 / 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-ELW / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsLeonardo-Silvestre, H. / McEwan, P.A. / Hymowitz, S.G.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Scaffold-Hopping Approach To Discover Potent, Selective, and Efficacious Inhibitors of NF-kappa B Inducing Kinase.
Authors: Blaquiere, N. / Castanedo, G.M. / Burch, J.D. / Berezhkovskiy, L.M. / Brightbill, H. / Brown, S. / Chan, C. / Chiang, P.C. / Crawford, J.J. / Dong, T. / Fan, P. / Feng, J. / Ghilardi, N. / ...Authors: Blaquiere, N. / Castanedo, G.M. / Burch, J.D. / Berezhkovskiy, L.M. / Brightbill, H. / Brown, S. / Chan, C. / Chiang, P.C. / Crawford, J.J. / Dong, T. / Fan, P. / Feng, J. / Ghilardi, N. / Godemann, R. / Gogol, E. / Grabbe, A. / Hole, A.J. / Hu, B. / Hymowitz, S.G. / Alaoui Ismaili, M.H. / Le, H. / Lee, P. / Lee, W. / Lin, X. / Liu, N. / McEwan, P.A. / McKenzie, B. / Silvestre, H.L. / Suto, E. / Sujatha-Bhaskar, S. / Wu, G. / Wu, L.C. / Zhang, Y. / Zhong, Z. / Staben, S.T.
History
DepositionMar 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Aug 22, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)77,8704
Polymers77,0872
Non-polymers7832
Water32418
1
A: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9352
Polymers38,5431
Non-polymers3911
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)38,9352
Polymers38,5431
Non-polymers3911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.830, 144.830, 46.530
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 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-ELW / 5-fluoranyl-1-[4-[2-[(3~{R})-1-methyl-3-oxidanyl-2-oxidanylidene-pyrrol-3-yl]ethynyl]pyridin-2-yl]indazole-3-carboxamide


Mass: 391.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14FN5O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.17 Å3/Da / Density % sol: 61.14 %
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: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.84→36.21 Å / Num. obs: 21715 / % possible obs: 98.1 % / Redundancy: 6.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.7
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.745 / Num. unique obs: 10567 / CC1/2: 0.84 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G3E

4g3e


Resolution: 2.84→36.21 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.876 / SU B: 39.116 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R: 1.348 / ESU R Free: 0.4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1171 5.1 %RANDOM
Rwork0.234 ---
obs0.237 21715 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 76.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.84→36.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 58 18 5096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195207
X-RAY DIFFRACTIONr_bond_other_d0.0010.024997
X-RAY DIFFRACTIONr_angle_refined_deg1.0521.997050
X-RAY DIFFRACTIONr_angle_other_deg0.701311540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4775643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01723.442215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31915900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6641537
X-RAY DIFFRACTIONr_chiral_restr0.0520.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021148
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_it2.176.3872584
X-RAY DIFFRACTIONr_mcbond_other2.1666.3862583
X-RAY DIFFRACTIONr_mcangle_it3.7379.5723220
X-RAY DIFFRACTIONr_mcangle_other3.7389.5733221
X-RAY DIFFRACTIONr_scbond_it2.1116.6822623
X-RAY DIFFRACTIONr_scbond_other2.1116.6822623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6319.9163830
X-RAY DIFFRACTIONr_long_range_B_refined6.09250.8115780
X-RAY DIFFRACTIONr_long_range_B_other6.09250.8165781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.84→2.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 76 -
Rwork0.301 1660 -
obs--99.88 %
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)
11.8159-0.8187-0.33710.76090.06080.44990.00220.01820.01220.06590.0238-0.03070.0217-0.0065-0.0260.09950.0139-0.02850.06660.05380.083540.462146.90951.5871
21.69940.41060.51321.1040.27221.51850.1118-0.14770.0719-0.0124-0.20530.14430.0061-0.06130.09350.0173-0.0242-0.01630.15530.04760.070912.763954.61843.52
31.74560.5196-0.45880.56790.1090.8188-0.04-0.02130.09470.00510.1180.03060.07970.0622-0.0780.08870.0062-0.05440.05590.03730.114267.911231.6399-4.2589
40.41740.13040.07972.3276-0.43851.6156-0.09780.0962-0.04620.06680.17190.20460.0197-0.0806-0.07410.08-0.0497-0.04180.07910.06670.124343.576917.6391-1.8957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A334 - 472
2X-RAY DIFFRACTION2A473 - 675
3X-RAY DIFFRACTION3B334 - 472
4X-RAY DIFFRACTION4B473 - 675

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