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- PDB-5h08: Human PTPRZ D1 domain complexed with NAZ2329 -

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Basic information

Entry
Database: PDB / ID: 5h08
TitleHuman PTPRZ D1 domain complexed with NAZ2329
ComponentsReceptor-type tyrosine-protein phosphatase zeta
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein Tyrosine Phosphatase / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


perineuronal net / regulation of oligodendrocyte progenitor proliferation / transmembrane receptor protein tyrosine phosphatase activity / regulation of myelination / Other interleukin signaling / positive regulation of oligodendrocyte differentiation / Signaling by ALK / oligodendrocyte differentiation / peptidyl-tyrosine dephosphorylation / hematopoietic progenitor cell differentiation ...perineuronal net / regulation of oligodendrocyte progenitor proliferation / transmembrane receptor protein tyrosine phosphatase activity / regulation of myelination / Other interleukin signaling / positive regulation of oligodendrocyte differentiation / Signaling by ALK / oligodendrocyte differentiation / peptidyl-tyrosine dephosphorylation / hematopoietic progenitor cell differentiation / axonogenesis / protein dephosphorylation / protein-tyrosine-phosphatase / central nervous system development / protein tyrosine phosphatase activity / integrin binding / negative regulation of neuron apoptotic process / learning or memory / synapse / extracellular region / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / 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. ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / 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 / Fibronectin type III domain / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-7WL / Receptor-type tyrosine-protein phosphatase zeta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSugawara, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and development15im0110409b0104 Japan
Citation
Journal: Sci Rep / Year: 2017
Title: Targeting PTPRZ inhibits stem cell-like properties and tumorigenicity in glioblastoma cells
Authors: Fujikawa, A. / Sugawara, H. / Tanaka, T. / Matsumoto, M. / Kuboyama, K. / Suzuki, R. / Tanga, N. / Ogata, A. / Masumura, M. / Noda, M.
#1: Journal: Scientific Reports / Year: 2016
Title: Small-molecule inhibition of PTPRZ suppresses tumor growth in a rat model of glioblastoma.
Authors: Fujikawa, A. / Nagahira, A. / Sugawara, H. / Ishii, K. / Imajo, S. / Matsumoto, M. / Kuboyama, K. / Suzuki, R. / Tanga, N. / Noda, M. / Uchiyama, S. / Tomoo, T. / Ogata, A. / Masumura, M. / Noda, M.
History
DepositionOct 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 8, 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: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4562
Polymers33,9541
Non-polymers5021
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13350 Å2
Unit cell
Length a, b, c (Å)53.776, 72.306, 90.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHIS PROTEIN IS ACTIVE MONOMER, HOWEVER IT DIMERIZES BY

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase zeta / R-PTP-zeta / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein-tyrosine ...R-PTP-zeta / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein-tyrosine phosphatase receptor type Z polypeptide 2 / R-PTP-zeta-2


Mass: 33954.402 Da / Num. of mol.: 1 / Fragment: UNP residues 1698-1993
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRZ1, HTPZP2, PTPRZ, PTPRZ2, PTPZ / Production host: Bombyx mori (domestic silkworm) / References: UniProt: P23471, protein-tyrosine-phosphatase
#2: Chemical ChemComp-7WL / 3-{[2-Ethoxy-5-(trifluoromethyl)benzyl]sulfanyl}-N-(phenylsulfonyl)thiophene-2-carboxamide


Mass: 501.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18F3NO4S3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ISOFORM 2 IN UNP P23471.

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10%(w/v) PEG8000, 20%(v/v) ethylene glycol, 30mM sodium fluoride, 30mM sodium bromide, 30mM sodium iodide. NAZ2329 was soaked into the crystal.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.53→100 Å / Num. obs: 10798 / % possible obs: 87.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AWX

5awx


Resolution: 2.53→45.4 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.852 / SU B: 25.429 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29689 536 5.1 %RANDOM
Rwork0.21029 ---
obs0.21476 9992 84.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.25 Å2
Baniso -1Baniso -2Baniso -3
1--29.55 Å20 Å20 Å2
2--11.65 Å20 Å2
3---17.9 Å2
Refinement stepCycle: 1 / Resolution: 2.53→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 32 14 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192367
X-RAY DIFFRACTIONr_bond_other_d0.0020.022129
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9443219
X-RAY DIFFRACTIONr_angle_other_deg1.08334926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8775280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66723.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40715384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9881514
X-RAY DIFFRACTIONr_chiral_restr0.1020.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212625
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02505
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_it0.7091.6111126
X-RAY DIFFRACTIONr_mcbond_other0.7091.6111125
X-RAY DIFFRACTIONr_mcangle_it1.2612.4151404
X-RAY DIFFRACTIONr_mcangle_other1.2612.4161405
X-RAY DIFFRACTIONr_scbond_it0.5281.6241241
X-RAY DIFFRACTIONr_scbond_other0.5291.6251242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9552.4271816
X-RAY DIFFRACTIONr_long_range_B_refined2.37718.4512679
X-RAY DIFFRACTIONr_long_range_B_other2.37618.4522680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.526→2.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 17 -
Rwork0.293 373 -
obs--42.9 %
Refinement TLS params.Method: refined / Origin x: 19.9262 Å / Origin y: 0.4235 Å / Origin z: 44.6027 Å
111213212223313233
T0.2331 Å20.0147 Å2-0.0195 Å2-0.039 Å2-0.0075 Å2--0.0354 Å2
L3.3654 °2-0.4957 °20.216 °2-3.2108 °20.8278 °2--2.2589 °2
S0.0244 Å °-0.0037 Å °-0.3331 Å °0.0552 Å °0.0697 Å °0.0245 Å °0.3861 Å °0.2686 Å °-0.0941 Å °

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