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- PDB-5k26: Structure of the SH3 domain of MLK3 bound to peptide generated fr... -

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Basic information

Entry
Database: PDB / ID: 5k26
TitleStructure of the SH3 domain of MLK3 bound to peptide generated from phage display
ComponentsMitogen-activated protein kinase kinase kinase 11,Chimera protein of MLK3-SH3 and MIP
KeywordsTRANSFERASE / MLK3 / SH3 / phage display / signalling protein
Function / homology
Function and homology information


mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / RHOV GTPase cycle / microtubule-based process / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity ...mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase kinase binding / mitogen-activated protein kinase kinase binding / RHOV GTPase cycle / microtubule-based process / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity / positive regulation of JUN kinase activity / JNK cascade / positive regulation of JNK cascade / RAF activation / small GTPase binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of neuron apoptotic process / MAPK cascade / microtubule / protein autophosphorylation / protein kinase activity / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein homodimerization activity / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / SH3 Domains / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Mainly Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKall, S.K. / Lavie, A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Identification of two distinct peptide-binding pockets in the SH3 domain of human mixed-lineage kinase 3.
Authors: Kokoszka, M.E. / Kall, S.L. / Khosla, S. / McGinnis, J.E. / Lavie, A. / Kay, B.K.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 11,Chimera protein of MLK3-SH3 and MIP
B: Mitogen-activated protein kinase kinase kinase 11,Chimera protein of MLK3-SH3 and MIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9183
Polymers18,7222
Non-polymers1951
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.000, 64.000, 35.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 11,Chimera protein of MLK3-SH3 and MIP / Mixed lineage kinase 3 / Src-homology 3 domain-containing proline-rich kinase


Mass: 9361.192 Da / Num. of mol.: 2
Fragment: SH3 domain (UNP residues 41-105),SH3 domain (UNP residues 41-105)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K11, MLK3, PTK1, SPRK / Production host: Escherichia coli (E. coli)
References: UniProt: Q16584, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.31 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Na-Phosphate, 0.1 M K-Phosphate, 0.1 M MES 6.5, 1.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.2→55.43 Å / Num. obs: 48242 / % possible obs: 97.2 % / Redundancy: 4.92 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.53
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.76 / % possible all: 83.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SEM

1sem


Resolution: 1.2→55.43 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.764 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16826 2412 4.9 %RANDOM
Rwork0.13712 ---
obs0.13865 46672 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å20 Å2
2---0.54 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.2→55.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 12 123 1296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0191292
X-RAY DIFFRACTIONr_bond_other_d0.0050.021171
X-RAY DIFFRACTIONr_angle_refined_deg3.0061.9281769
X-RAY DIFFRACTIONr_angle_other_deg1.58532685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60623.23568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76415186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0481515
X-RAY DIFFRACTIONr_chiral_restr0.1780.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211571
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02336
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_it3.4751.675646
X-RAY DIFFRACTIONr_mcbond_other3.4591.666645
X-RAY DIFFRACTIONr_mcangle_it4.3082.513813
X-RAY DIFFRACTIONr_mcangle_other4.3262.518814
X-RAY DIFFRACTIONr_scbond_it7.92.172646
X-RAY DIFFRACTIONr_scbond_other7.9012.171646
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.0043.101951
X-RAY DIFFRACTIONr_long_range_B_refined9.8515.2111429
X-RAY DIFFRACTIONr_long_range_B_other9.84715.2221430
X-RAY DIFFRACTIONr_rigid_bond_restr7.21432463
X-RAY DIFFRACTIONr_sphericity_free32.597544
X-RAY DIFFRACTIONr_sphericity_bonded21.6252502
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 115 -
Rwork0.278 2666 -
obs--73.92 %

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