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- PDB-4y85: Crystal structure of COT kinase domain in complex with 5-(5-(1H-i... -

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Basic information

Entry
Database: PDB / ID: 4y85
TitleCrystal structure of COT kinase domain in complex with 5-(5-(1H-indol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-1,3,4-oxadiazol-2-amine
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-499 / Mitogen-activated protein kinase kinase kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 1.3Jun 27, 2018Group: Data collection / Derived calculations / Category: struct_conn / Item: _struct_conn.pdbx_dist_value
Revision 1.4Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5May 29, 2019Group: Data collection / Derived calculations / Category: struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)113,8556
Polymers112,9063
Non-polymers9493
Water6,503361
1
A: Mitogen-activated protein kinase kinase kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9522
Polymers37,6351
Non-polymers3161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9522
Polymers37,6351
Non-polymers3161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mitogen-activated protein kinase kinase kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9522
Polymers37,6351
Non-polymers3161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.978, 85.113, 85.964
Angle α, β, γ (deg.)90.000, 91.060, 90.000
Int Tables number5
Space group name H-MC121

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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 / Fragment: UNP resdiues 36-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K8, COT, ESTF / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P41279, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-499 / 5-[5-(1H-indol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-1,3,4-oxadiazol-2-amine


Mass: 316.317 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H12N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1 M HEPES pH 7.2, 24% PEGMME 550, 0.05 M MgCl2

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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: Apr 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→73.77 Å / Num. obs: 45307 / % possible obs: 99 % / Redundancy: 3.72 % / Rsym value: 0.104 / Net I/σ(I): 10.55
Reflection shellResolution: 2.33→2.4 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.27 / % possible all: 94

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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: 2.33→46.6 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9113 / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.28 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2265 5 %RANDOM
Rwork0.1772 ---
obs0.1787 45305 99.04 %-
Displacement parametersBiso max: 135.47 Å2 / Biso mean: 34.49 Å2 / Biso min: 5.94 Å2
Baniso -1Baniso -2Baniso -3
1-4.6172 Å20 Å2-0.9278 Å2
2--3.8953 Å20 Å2
3----8.5125 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: final / Resolution: 2.33→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6939 0 72 361 7372
Biso mean--19.68 36.25 -
Num. residues----916
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2311SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes125HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1171HARMONIC5
X-RAY DIFFRACTIONt_it7198HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion958SEMIHARMONIC5
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_contact8212SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7198HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg9813HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion17.51
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2525 157 5 %
Rwork0.2038 2986 -
all0.2063 3143 -
obs--99.04 %
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)
10.76290.22480.11892.10850.20530.539-0.0121-0.03410.0960.03280.0016-0.1148-0.0183-0.04580.0105-0.1307-0.002-0.0059-0.1163-0.0019-0.046620.32244.3193194.1522
22.64790.637-0.43141.0721-0.07030.32140.04310.01840.1023-0.0088-0.00840.25280.0335-0.0236-0.0347-0.14470.0068-0.0142-0.1502-0.0103-0.0232-3.875146.6846194.8587
32.6450.70010.37111.67590.37450.42880.0540.0588-0.4460.0111-0.03040.0721-0.047-0.0495-0.0236-0.1530.0181-0.0071-0.1739-0.0014-0.04620.99074.8519234.4064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A73 - 390
2X-RAY DIFFRACTION2{ B|* }B73 - 390
3X-RAY DIFFRACTION3{ C|* }C73 - 390

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