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- PDB-5t8o: Crystal structure of murine NF-kappaB inducing kinase (NIK) bound... -

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Basic information

Entry
Database: PDB / ID: 5t8o
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) bound to Imidazobenzoxepin Compound 3
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-76Z / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsSmith, M.A. / McEwan, P. / 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: PDBE / 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

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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)78,38211
Polymers77,0872
Non-polymers1,2959
Water5,152286
1
A: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2396
Polymers38,5431
Non-polymers6965
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)39,1435
Polymers38,5431
Non-polymers6004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.950, 143.950, 45.470
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-76Z / 10-(3-methyl-3-oxidanyl-but-1-ynyl)-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepine-2-carboxamide


Mass: 311.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N3O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→50.89 Å / Num. obs: 34595 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.5
Reflection shellResolution: 2.41→2.54 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→143.95 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.89 / SU B: 16.556 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25566 3549 10.3 %RANDOM
Rwork0.20145 ---
obs0.20682 31025 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.41→143.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 81 286 5434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195291
X-RAY DIFFRACTIONr_bond_other_d0.0020.025059
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.997165
X-RAY DIFFRACTIONr_angle_other_deg0.937311684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96323.318220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20915912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6821538
X-RAY DIFFRACTIONr_chiral_restr0.070.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215854
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021166
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_it0.431.672609
X-RAY DIFFRACTIONr_mcbond_other0.431.672610
X-RAY DIFFRACTIONr_mcangle_it0.7842.5013256
X-RAY DIFFRACTIONr_mcangle_other0.7842.5023256
X-RAY DIFFRACTIONr_scbond_it0.3931.7612682
X-RAY DIFFRACTIONr_scbond_other0.3931.7612683
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.652.6233907
X-RAY DIFFRACTIONr_long_range_B_refined3.48413.6835948
X-RAY DIFFRACTIONr_long_range_B_other3.4113.6065923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 271 -
Rwork0.292 2259 -
obs--94.65 %
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)
16.2268-1.92141.05994.0744-0.61444.3331-0.07080.0153-0.11830.1149-0.09520.0411-0.00430.0460.1660.0075-0.00330.0010.01880.0360.086228.36428.142.802
26.5094-0.2684-0.77820.6018-0.12450.8829-0.04090.16960.169-0.036-0.04340.0871-0.13880.03860.08420.06410.0113-0.01050.02610.02360.059945.221.4910.51
35.07171.1022-3.33363.4259-0.81977.5004-0.0227-0.6313-0.42360.3025-0.1436-0.26330.44940.43650.16620.06770.0054-0.02840.16120.0820.080662.96615.9497.59
46.8228-0.2225-0.19833.63210.52244.538-0.02810.0629-0.1005-0.02170.0969-0.1273-0.0287-0.0575-0.06880.02710.002-0.03850.0054-0.00430.07870.12940.219-2.891
55.10982.5091-0.11174.5601-0.44210.7697-0.12590.1510.1301-0.12720.0340.1935-0.2405-0.0330.09180.10690.0199-0.04160.0143-0.00130.025417.09447.661-3.933
64.2773-1.0178-1.1255.96410.79146.51030.0143-0.17820.14180.10830.1139-0.77420.01040.73-0.12820.0912-0.0315-0.01970.0967-0.02220.120734.25155.420.865
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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