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- PDB-6aqb: Structure of the SH3 domain of MLK3 bound to peptide generated fr... -

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Basic information

Entry
Database: PDB / ID: 6aqb
TitleStructure of the SH3 domain of MLK3 bound to peptide generated from phage display
ComponentsChimera protein of MLK3-SH3 and MIP (E.C.2.7.11.25)
KeywordsTRANSFERASE / MLK3 / SH3 / phage display / signalling protein
Function / homology
Function and homology information


positive regulation of JUN kinase activity / mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / RHOV GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity ...positive regulation of JUN kinase activity / mitogen-activated protein kinase kinase kinase / cell cycle G1/S phase transition / JUN kinase kinase kinase activity / mitogen-activated protein kinase kinase binding / mitogen-activated protein kinase kinase kinase binding / RHOV GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / MAP kinase kinase kinase activity / microtubule-based process / JNK cascade / RAF activation / positive regulation of JNK cascade / 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 / protein autophosphorylation / microtubule / protein phosphorylation / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / protein homodimerization activity / ATP binding / membrane / identical protein binding / cytoplasm / cytosol
Similarity search - Function
MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / 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 ...MLK1-3, SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase, MLK1-4 / Variant SH3 domain / : / 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 / 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
Similarity search - Domain/homology
PHOSPHATE ION / Mitogen-activated protein kinase kinase kinase 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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
DepositionAug 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: 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 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of MLK3-SH3 and MIP (E.C.2.7.11.25)
B: Chimera protein of MLK3-SH3 and MIP (E.C.2.7.11.25)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9547
Polymers15,6112
Non-polymers3435
Water1,802100
1
A: Chimera protein of MLK3-SH3 and MIP (E.C.2.7.11.25)
hetero molecules

B: Chimera protein of MLK3-SH3 and MIP (E.C.2.7.11.25)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9547
Polymers15,6112
Non-polymers3435
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3200 Å2
ΔGint-6 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.510, 45.740, 49.660
Angle α, β, γ (deg.)90.00, 120.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chimera protein of MLK3-SH3 and MIP (E.C.2.7.11.25) / Mixed lineage kinase 3 / Src-homology 3 domain-containing proline-rich kinase


Mass: 7805.560 Da / Num. of mol.: 2 / Fragment: 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M NaH2PO4 0.1 M KH2PO4 0.1 M MES pH 6.5 1.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078185 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078185 Å / Relative weight: 1
ReflectionResolution: 1.5→42.62 Å / Num. obs: 44942 / % possible obs: 90.9 % / Redundancy: 1.8 % / Net I/σ(I): 9.94
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 1.83 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 6942 / CC1/2: 0.848 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOLREPphasing
ARPmodel building
RefinementResolution: 1.5→42.62 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.909 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22761 1181 5 %RANDOM
Rwork0.18745 ---
obs0.18938 22557 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.655 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0.48 Å2
2---0.02 Å20 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.5→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 21 100 1179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021108
X-RAY DIFFRACTIONr_bond_other_d0.0030.02992
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.9671506
X-RAY DIFFRACTIONr_angle_other_deg1.09232298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4455138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14623.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.06315144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9671510
X-RAY DIFFRACTIONr_chiral_restr0.1190.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02236
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_it3.1852.574558
X-RAY DIFFRACTIONr_mcbond_other3.1772.571557
X-RAY DIFFRACTIONr_mcangle_it4.2843.842694
X-RAY DIFFRACTIONr_mcangle_other4.2863.845695
X-RAY DIFFRACTIONr_scbond_it4.3472.96550
X-RAY DIFFRACTIONr_scbond_other3.7722.949546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6524.211807
X-RAY DIFFRACTIONr_long_range_B_refined10.65632.3481248
X-RAY DIFFRACTIONr_long_range_B_other10.65232.3791249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 94 -
Rwork0.354 1718 -
obs--98.42 %

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