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- PDB-5wnj: Crystal structure of murine receptor-interacting protein kinase 4... -

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Basic information

Entry
Database: PDB / ID: 5wnj
TitleCrystal structure of murine receptor-interacting protein kinase 4 (Ripk4) D143N in complex with lestaurtinib
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 / phosphorylation / 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
Lestaurtinib / Receptor-interacting serine/threonine-protein kinase 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 2.0Dec 7, 2022Group: Database references / Non-polymer description / Structure summary
Category: chem_comp / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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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)39,4633
Polymers38,9881
Non-polymers4752
Water43224
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)78,9266
Polymers77,9762
Non-polymers9504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area2970 Å2
ΔGint-28 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.825, 110.247, 145.536
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-2V9 / Lestaurtinib / (5S,6S,8R)-6-hydroxy-6-(hydroxymethyl)-5-methyl-5,6,7,8-tetrahydro-13H-5,8-epoxy-4b,8a,14-triazadibenzo[b,h]cycloocta[1,2,3,4-jkl]cyclopenta[e]-as-indacen-13-one / Lestaurtinib


Mass: 439.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N3O4 / Comment: inhibitor*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 66.24 %
Crystal growTemperature: 292 K / Method: microbatch
Details: 0.1M HEPES pH 7.5, 0.2M magnesium chloride, 10% 2-propanol, 15% ethylene glycol, 10% PEG4000

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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: 2.55→50.01 Å / Num. obs: 18791 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→50.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.865 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25226 912 4.9 %RANDOM
Rwork0.2195 ---
obs0.22105 17877 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.227 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å20 Å2
2--1.05 Å20 Å2
3----4.03 Å2
Refinement stepCycle: 1 / Resolution: 2.55→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 34 24 2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192137
X-RAY DIFFRACTIONr_bond_other_d0.0010.021942
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.9582917
X-RAY DIFFRACTIONr_angle_other_deg0.9072.9884481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95822.85784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72115336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5821513
X-RAY DIFFRACTIONr_chiral_restr0.0680.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212361
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
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_it3.1956.6621053
X-RAY DIFFRACTIONr_mcbond_other3.1766.6581052
X-RAY DIFFRACTIONr_mcangle_it5.1229.9671311
X-RAY DIFFRACTIONr_mcangle_other5.129.9731312
X-RAY DIFFRACTIONr_scbond_it2.9996.5791084
X-RAY DIFFRACTIONr_scbond_other2.9986.5791085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8169.771607
X-RAY DIFFRACTIONr_long_range_B_refined7.13973.8742343
X-RAY DIFFRACTIONr_long_range_B_other7.13773.8572344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.553→2.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 69 -
Rwork0.307 1253 -
obs--96.22 %

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