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- PDB-5ovx: X-Ray Characterization of Striatal-Enriched Protein Tyrosine Phos... -

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Basic information

Entry
Database: PDB / ID: 5ovx
TitleX-Ray Characterization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors
ComponentsTyrosine-protein phosphatase non-receptor type 5
KeywordsHYDROLASE / Phosphatase / Alzheimer's disease / Inhibitor / PTPN5
Function / homology
Function and homology information


Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm ...Interleukin-37 signaling / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-AY5 / Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKack, H. / Wissler, L.
CitationJournal: J. Med. Chem. / Year: 2017
Title: X-ray Characterization and Structure-Based Optimization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors.
Authors: Witten, M.R. / Wissler, L. / Snow, M. / Geschwindner, S. / Read, J.A. / Brandon, N.J. / Nairn, A.C. / Lombroso, P.J. / Kack, H. / Ellman, J.A.
History
DepositionAug 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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: Tyrosine-protein phosphatase non-receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6602
Polymers35,2211
Non-polymers4391
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.117, 64.124, 100.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 5 / Neural-specific protein-tyrosine phosphatase / Striatum-enriched protein-tyrosine phosphatase / STEP


Mass: 35220.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN5 / Production host: Escherichia coli (E. coli) / References: UniProt: P54829, protein-tyrosine-phosphatase
#2: Chemical ChemComp-AY5 / [(~{S})-[4-[3-[(~{S})-(3,4-dichlorophenyl)-oxidanyl-methyl]phenyl]phenyl]-oxidanyl-methyl]phosphonic acid


Mass: 439.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17Cl2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 26-28% PEG3350, 0.1M Bis-Tris pH5.5, 0.2M Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→100.34 Å / Num. obs: 20322 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Rrim(I) all: 0.111 / Net I/σ(I): 18.7 / Num. measured all: 141734 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1670.51116440.8950.2090.552100
8.91-100.345.60.0263220.9990.0120.02998.7

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Processing

Software
NameVersionClassification
Aimless0.2.8data scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BV5

2bv5


Resolution: 2.1→21.85 Å / Cor.coef. Fo:Fc: 0.9188 / Cor.coef. Fo:Fc free: 0.9015 / SU R Cruickshank DPI: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1036 5.12 %RANDOM
Rwork0.1954 ---
obs0.197 20246 99.97 %-
Displacement parametersBiso max: 111.27 Å2 / Biso mean: 27.5 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.2055 Å20 Å20 Å2
2--1.8349 Å20 Å2
3---0.3706 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: final / Resolution: 2.1→21.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 28 252 2610
Biso mean--35.26 38.26 -
Num. residues----287
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d837SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes354HARMONIC5
X-RAY DIFFRACTIONt_it2429HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion312SEMIHARMONIC5
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_contact2910SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2429HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3306HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion17.05
LS refinement shellResolution: 2.1→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2494 164 5.64 %
Rwork0.175 2746 -
all0.1789 2910 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 14.688 Å / Origin y: -5.095 Å / Origin z: -15.7047 Å
111213212223313233
T-0.0524 Å20.0143 Å20.0239 Å2--0.1022 Å20.0219 Å2---0.0489 Å2
L1.2618 °2-0.0386 °2-0.7274 °2-1.0996 °2-0.2748 °2--1.9268 °2
S0.0401 Å °0.0093 Å °-0.0138 Å °0.0146 Å °0.0247 Å °0.1581 Å °-0.0824 Å °-0.1573 Å °-0.0648 Å °
Refinement TLS groupSelection details: { A|* }

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