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- PDB-6x3l: Sortilin-Progranulin Interaction With Compound 2 -

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Basic information

Entry
Database: PDB / ID: 6x3l
TitleSortilin-Progranulin Interaction With Compound 2
ComponentsSortilin
KeywordsUNKNOWN FUNCTION / Protein Protein Interaction
Function / homology
Function and homology information


neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / Golgi to lysosome transport / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity ...neurotensin receptor activity, non-G protein-coupled / negative regulation of lipoprotein lipase activity / Golgi to lysosome transport / myotube differentiation / cerebellar climbing fiber to Purkinje cell synapse / plasma membrane to endosome transport / retromer complex binding / maintenance of synapse structure / Golgi to endosome transport / nerve growth factor receptor activity / vesicle organization / endosome transport via multivesicular body sorting pathway / nerve growth factor binding / protein targeting to lysosome / trans-Golgi network transport vesicle / clathrin-coated vesicle / Golgi cisterna membrane / Golgi Associated Vesicle Biogenesis / negative regulation of fat cell differentiation / endosome to lysosome transport / glucose import / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / neuropeptide signaling pathway / clathrin-coated pit / ossification / response to insulin / endocytosis / cytoplasmic vesicle / regulation of gene expression / nuclear membrane / lysosome / early endosome / endosome membrane / G protein-coupled receptor signaling pathway / lysosomal membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / membrane / plasma membrane / cytosol
Similarity search - Function
VPS10 / Sortilin, C-terminal / Sortilin, N-terminal / Sortilin, neurotensin receptor 3, C-terminal / Sortilin, neurotensin receptor 3, / VPS10 / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsParthasarathy, G. / Soisson, S.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Identification of potent inhibitors of the sortilin-progranulin interaction.
Authors: Stachel, S.J. / Ginnetti, A.T. / Johnson, S.A. / Cramer, P. / Wang, Y. / Bukhtiyarova, M. / Krosky, D. / Stump, C. / Hurzy, D.M. / Schlegel, K.A. / Cooke, A.J. / Allen, S. / O'Donnell, G. / ...Authors: Stachel, S.J. / Ginnetti, A.T. / Johnson, S.A. / Cramer, P. / Wang, Y. / Bukhtiyarova, M. / Krosky, D. / Stump, C. / Hurzy, D.M. / Schlegel, K.A. / Cooke, A.J. / Allen, S. / O'Donnell, G. / Ziebell, M. / Parthasarathy, G. / Getty, K.L. / Ho, T. / Ou, Y. / Jovanovska, A. / Carroll, S.S. / Pausch, M. / Lumb, K. / Mosser, S.D. / Voleti, B. / Klein, D.J. / Soisson, S.M. / Zerbinatti, C. / Coleman, P.J.
History
DepositionMay 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Sortilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1905
Polymers84,9911
Non-polymers1,1994
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.832, 75.513, 110.984
Angle α, β, γ (deg.)90.000, 127.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sortilin / 100 kDa NT receptor / Glycoprotein 95 / Gp95 / Neurotensin receptor 3 / NTR3


Mass: 84991.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORT1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q99523
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-UMJ / 1-benzyl-3-tert-butyl-1H-pyrazole-5-carboxylic acid


Mass: 258.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20-25% PEG3350, 0.4M Na Malonate, pH8, 0.1M Tris, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→46.24 Å / Num. obs: 29077 / % possible obs: 98.39 % / Redundancy: 15 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.8
Reflection shellResolution: 2.89→2.9 Å / Rmerge(I) obs: 0.271 / Num. unique obs: 187

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
HKL-3000data scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F6K

3f6k


Resolution: 2.7→46.24 Å / Cor.coef. Fo:Fc: 0.9082 / Cor.coef. Fo:Fc free: 0.8777 / SU R Cruickshank DPI: 0.472 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.437 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.309
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 1488 5.12 %RANDOM
Rwork0.2166 ---
obs0.2194 29077 98.39 %-
Displacement parametersBiso max: 187.17 Å2 / Biso mean: 96.54 Å2 / Biso min: 41.88 Å2
Baniso -1Baniso -2Baniso -3
1-33.5807 Å20 Å20.6088 Å2
2---30.563 Å20 Å2
3----3.0177 Å2
Refine analyzeLuzzati coordinate error obs: 0.462 Å
Refinement stepCycle: final / Resolution: 2.7→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5143 0 81 24 5248
Biso mean--91.04 76.75 -
Num. residues----654
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1846SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes132HARMONIC8
X-RAY DIFFRACTIONt_gen_planes791HARMONIC8
X-RAY DIFFRACTIONt_it5347HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion704SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5964SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5347HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7247HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion2.21
X-RAY DIFFRACTIONt_other_torsion21.38
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3004 132 5.32 %
Rwork0.2506 2349 -
all0.2531 2481 -
obs--98.39 %

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