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- PDB-4y83: Crystal structure of COT kinase domain in complex with 5-(2-amino... -

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Basic information

Entry
Database: PDB / ID: 4y83
TitleCrystal structure of COT kinase domain in complex with 5-(2-amino-5-(quinolin-3-yl)pyridin-3-yl)-1,3,4-oxadiazole-2(3H)-thione
ComponentsMitogen-activated protein kinase kinase kinase 8
KeywordsTRANSFERASE / COT / Tpl-2 / MAP3K8 / kinase / inhibitor / complex
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / T cell costimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding ...mitogen-activated protein kinase kinase kinase / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / T cell costimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 8 / 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 domain profile. ...Mitogen-activated protein (MAP) kinase kinase kinase 8 / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-49B / Mitogen-activated protein kinase kinase kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsGutmann, S. / Hinniger, A.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Crystal Structure of Cancer Osaka Thyroid Kinase Reveals an Unexpected Kinase Domain Fold.
Authors: Gutmann, S. / Hinniger, A. / Fendrich, G. / Druckes, P. / Antz, S. / Mattes, H. / Mobitz, H. / Ofner, S. / Schmiedeberg, N. / Stojanovic, A. / Rieffel, S. / Strauss, A. / Troxler, T. / Glatthar, R. / Sparrer, H.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 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

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 8
B: Mitogen-activated protein kinase kinase kinase 8
C: Mitogen-activated protein kinase kinase kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8706
Polymers112,9063
Non-polymers9643
Water3,009167
1
A: Mitogen-activated protein kinase kinase kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9572
Polymers37,6351
Non-polymers3211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase kinase kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9572
Polymers37,6351
Non-polymers3211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mitogen-activated protein kinase kinase kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9572
Polymers37,6351
Non-polymers3211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.952, 101.952, 108.315
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 8 / Cancer Osaka thyroid oncogene / Proto-oncogene c-Cot / Serine/threonine-protein kinase cot / Tumor ...Cancer Osaka thyroid oncogene / Proto-oncogene c-Cot / Serine/threonine-protein kinase cot / Tumor progression locus 2 / TPL-2


Mass: 37635.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K8, COT, ESTF / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21
References: UniProt: P41279, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-49B / 5-[2-amino-5-(quinolin-3-yl)pyridin-3-yl]-1,3,4-oxadiazole-2(3H)-thione


Mass: 321.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H11N5OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: Reservoir solution: 8% (w/v) PEG4000, 12% (v/v) ethylene glycol, 7% (v/v) iso-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→88.31 Å / Num. obs: 28213 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.76 % / Biso Wilson estimate: 76.04 Å2 / Rmerge F obs: 0.074 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.097 / Rsym value: 0.088 / Net I/av σ(I): 14.7 / Net I/σ(I): 14.72 / Num. measured all: 162522
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.89-2.970.2950.4483.6712909221722170.492100
2.97-3.070.2350.3664.4714479248524850.402100
3.07-3.170.1940.2925.5312485214321430.32100
3.17-3.290.1460.2187.513221226922690.239100
3.29-3.410.1090.1669.6411311194219420.183100
3.41-3.560.0850.13611.6611927205320530.15100
3.56-3.720.0770.12413.7710871190719070.136100
3.72-3.910.0580.09516.4710643184518450.104100
3.91-4.140.0470.0819.0310109175917590.089100
4.14-4.40.0410.07421.559327163216320.082100
4.4-4.730.0380.0723.428670153415340.077100
4.73-5.140.0390.0722.868005141414140.077100
5.14-5.680.0360.06523.337465130613060.071100
5.68-6.430.0360.06323.566654116011600.069100
6.43-7.590.030.05325.9856399849840.058100
7.59-9.720.0230.04329.6446208188180.047100
9.72-15.380.0220.04331.4431775615610.047100
15.38-88.310.0190.03430.7810101881840.03897.9

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.5refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→88.29 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.8648 / SU R Cruickshank DPI: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.737 / SU Rfree Blow DPI: 0.316 / SU Rfree Cruickshank DPI: 0.328
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 1411 5 %RANDOM
Rwork0.2017 ---
obs0.2037 28212 99.99 %-
Displacement parametersBiso max: 156.32 Å2 / Biso mean: 61.77 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.2199 Å20 Å20 Å2
2--0.2199 Å20 Å2
3----0.4398 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: final / Resolution: 2.89→88.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6124 0 69 167 6360
Biso mean--39.31 47 -
Num. residues----894
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1846SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1005HARMONIC5
X-RAY DIFFRACTIONt_it6339HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion888SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6799SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6339HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8665HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion18.56
LS refinement shellResolution: 2.89→3 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.27 151 5.01 %
Rwork0.2119 2861 -
all0.2149 3012 -
obs--99.99 %
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)
13.9825-0.53380.92171.2984-0.22013.343-0.21710.1632-0.05-0.04180.1839-0.19260.30650.06080.0332-0.3412-0.02720.0166-0.3417-0.075-0.3837-0.6497-8.1952-6.952
22.422-0.82060.28572.2807-0.89433.7146-0.01310.11730.12030.24810.05030.21570.1875-0.2137-0.0371-0.3393-0.00150.0748-0.40610.0007-0.385643.5562-33.8076-24.1096
33.16980.37420.36693.2713-2.31094.3283-0.4433-0.1795-0.5087-0.25620.0174-0.09470.00010.47490.4259-0.4984-0.02450.101-0.2758-0.0027-0.33598.8532-62.5928-7.7941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A73 - 389
2X-RAY DIFFRACTION2{ B|* }B73 - 390
3X-RAY DIFFRACTION3{ C|* }C74 - 389

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