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- PDB-6e2o: ASK1 kinase domain complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6e2o
TitleASK1 kinase domain complex with inhibitor
ComponentsMitogen-activated protein kinase kinase kinase 5
KeywordsTRANSFERASE/INHIBITOR / protein kinase / inhibitor complex / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress ...cellular response to reactive nitrogen species / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / IRE1-TRAF2-ASK1 complex / protein kinase complex / mitogen-activated protein kinase kinase kinase / programmed necrotic cell death / JUN kinase kinase kinase activity / endothelial cell apoptotic process / positive regulation of p38MAPK cascade / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of cardiac muscle cell apoptotic process / p38MAPK cascade / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / MAP kinase kinase kinase activity / positive regulation of protein kinase activity / positive regulation of myoblast differentiation / stress-activated MAPK cascade / positive regulation of JUN kinase activity / JNK cascade / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to amino acid starvation / response to endoplasmic reticulum stress / response to ischemia / apoptotic signaling pathway / positive regulation of JNK cascade / cellular response to hydrogen peroxide / MAPK cascade / cellular senescence / cellular response to tumor necrosis factor / protein phosphatase binding / neuron apoptotic process / Oxidative Stress Induced Senescence / protein kinase activity / positive regulation of apoptotic process / protein domain specific binding / external side of plasma membrane / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / Transferase(Phosphotransferase) domain 1 ...MAP3K, deoxyribohydrolase domain / MAP3K, HisK-N-like globin domain / HisK-N-like globin domain of the ASK signalosome / Deoxyribohydrolase (DRHyd) domain of the ASK signalosome / MAP3K, TRAFs-binding domain / MAP3K, PH domain / MAP3K TRAFs-binding domain / ASK kinase PH domain / Sterile alpha motif/pointed domain superfamily / 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-S0L / Mitogen-activated protein kinase kinase kinase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.389 Å
AuthorsLansdon, E.B.
CitationJournal: J. Clin. Invest. / Year: 2018
Title: ASK1 contributes to fibrosis and dysfunction in models of kidney disease.
Authors: Liles, J.T. / Corkey, B.K. / Notte, G.T. / Budas, G.R. / Lansdon, E.B. / Hinojosa-Kirschenbaum, F. / Badal, S.S. / Lee, M. / Schultz, B.E. / Wise, S. / Pendem, S. / Graupe, M. / Castonguay, ...Authors: Liles, J.T. / Corkey, B.K. / Notte, G.T. / Budas, G.R. / Lansdon, E.B. / Hinojosa-Kirschenbaum, F. / Badal, S.S. / Lee, M. / Schultz, B.E. / Wise, S. / Pendem, S. / Graupe, M. / Castonguay, L. / Koch, K.A. / Wong, M.H. / Papalia, G.A. / French, D.M. / Sullivan, T. / Huntzicker, E.G. / Ma, F.Y. / Nikolic-Paterson, D.J. / Altuhaifi, T. / Yang, H. / Fogo, A.B. / Breckenridge, D.G.
History
DepositionJul 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 5
B: Mitogen-activated protein kinase kinase kinase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2304
Polymers66,4072
Non-polymers8232
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-7 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.632, 106.637, 156.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1131-

HOH

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 5 / Apoptosis signal-regulating kinase 1 / ASK-1 / MAPK/ERK kinase kinase 5 / MEKK 5


Mass: 33203.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K5, ASK1, MAPKKK5, MEKK5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99683, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-S0L / 4-(4-cyclopropyl-1H-imidazol-1-yl)-N-[3-(4-cyclopropyl-4H-1,2,4-triazol-3-yl)phenyl]pyridine-2-carboxamide


Mass: 411.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C23H21N7O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24% PEG 400, 3% PPE 400, 100mM Bis-Tris pH 7.5, 10mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 61441 / % possible obs: 99 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.7
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1990 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.389→46.856 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.39
RfactorNum. reflection% reflection
Rfree0.2676 1996 7.58 %
Rwork0.2126 --
obs0.2168 26343 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.389→46.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 62 69 4207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014236
X-RAY DIFFRACTIONf_angle_d1.1245717
X-RAY DIFFRACTIONf_dihedral_angle_d21.7812551
X-RAY DIFFRACTIONf_chiral_restr0.061609
X-RAY DIFFRACTIONf_plane_restr0.007730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3886-2.44840.38091300.28871587X-RAY DIFFRACTION89
2.4484-2.51460.36611350.26941648X-RAY DIFFRACTION94
2.5146-2.58850.30571380.24471688X-RAY DIFFRACTION96
2.5885-2.67210.29951400.23031702X-RAY DIFFRACTION96
2.6721-2.76760.331410.23191729X-RAY DIFFRACTION97
2.7676-2.87840.31121410.23141724X-RAY DIFFRACTION97
2.8784-3.00940.30721430.23441743X-RAY DIFFRACTION97
3.0094-3.1680.32151420.24261730X-RAY DIFFRACTION98
3.168-3.36640.30021450.23131761X-RAY DIFFRACTION98
3.3664-3.62620.28791460.21991781X-RAY DIFFRACTION99
3.6262-3.9910.23431460.20331785X-RAY DIFFRACTION99
3.991-4.56810.23321470.17691777X-RAY DIFFRACTION98
4.5681-5.75360.25771480.19791811X-RAY DIFFRACTION98
5.7536-46.86460.21821540.20021881X-RAY DIFFRACTION96

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