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- PDB-5wnm: Crystal structure of murine receptor-interacting protein 4 (Ripk4... -

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Basic information

Entry
Database: PDB / ID: 5wnm
TitleCrystal structure of murine receptor-interacting protein 4 (Ripk4) D143N bound to tozasertib (VX-680)
ComponentsReceptor-interacting serine/threonine-protein kinase 4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Inhibitor / Complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


morphogenesis of an epithelium / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / membrane / cytoplasm
Similarity search - Function
Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site ...Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-VX6 / Receptor-interacting serine/threonine-protein kinase 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuang, C.S. / Hymowitz, S.G.
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of Ripk4 Reveals Dimerization-Dependent Kinase Activity.
Authors: Huang, C.S. / Oberbeck, N. / Hsiao, Y.C. / Liu, P. / Johnson, A.R. / Dixit, V.M. / Hymowitz, S.G.
History
DepositionAug 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 13, 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

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4883
Polymers38,9881
Non-polymers5002
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Receptor-interacting serine/threonine-protein kinase 4
hetero molecules

A: Receptor-interacting serine/threonine-protein kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9766
Polymers77,9762
Non-polymers1,0004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area4670 Å2
ΔGint-29 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 109.612, 146.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 4 / Ankyrin repeat domain-containing protein 3 / PKC-associated protein kinase / PKC-regulated protein kinase


Mass: 38988.039 Da / Num. of mol.: 1 / Fragment: residues 1-342 / Mutation: D143N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk4, Ankrd3, Pkk / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9ERK0, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-VX6 / CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE


Mass: 464.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N8OS / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 292 K / Method: microbatch
Details: 0.1M HEPES pH 7.5, 200 mM magnesium chloride, 10% isopropanol, 15% ethylene glycol, and 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50.01 Å / Num. obs: 33710 / % possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 32.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.297 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26431 845 4.7 %RANDOM
Rwork0.22788 ---
obs0.2296 17007 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.188 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å20 Å2
2--2.86 Å20 Å2
3----4.76 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 34 30 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192123
X-RAY DIFFRACTIONr_bond_other_d0.0010.021924
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9532889
X-RAY DIFFRACTIONr_angle_other_deg0.9072.984437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37622.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96615327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5061513
X-RAY DIFFRACTIONr_chiral_restr0.0690.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212339
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02441
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_it2.8597.041049
X-RAY DIFFRACTIONr_mcbond_other2.8487.0361048
X-RAY DIFFRACTIONr_mcangle_it4.69610.5411306
X-RAY DIFFRACTIONr_mcangle_other4.69410.5461307
X-RAY DIFFRACTIONr_scbond_it2.596.9331074
X-RAY DIFFRACTIONr_scbond_other2.5886.9341075
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.24310.3391581
X-RAY DIFFRACTIONr_long_range_B_refined6.25778.8122264
X-RAY DIFFRACTIONr_long_range_B_other6.23978.8022264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 61 -
Rwork0.329 1194 -
obs--98.12 %

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