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- PDB-6h8r: CRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5... -

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Basic information

Entry
Database: PDB / ID: 6h8r
TitleCRYSTAL STRUCTURE OF THE HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5 (STEP) IN COMPLEX WITH COMPOUND 2
ComponentsTyrosine-protein phosphatase non-receptor type 5
KeywordsHYDROLASE / PROTEIN PHOSPHATASE / PTN5 / STEP / ALLOSTERIC MODULATOR
Function / homology
Function and homology information


Interleukin-37 signaling / protein dephosphorylation / phosphotyrosine residue binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell junction / endoplasmic reticulum membrane / protein kinase binding / signal transduction / nucleoplasm ...Interleukin-37 signaling / protein dephosphorylation / phosphotyrosine residue binding / 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-FWB / Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsHoerer, S. / Fiegen, D. / Schnapp, G.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Allosteric Activation of Striatal-Enriched Protein Tyrosine Phosphatase (STEP, PTPN5) by a Fragment-like Molecule.
Authors: Tautermann, C.S. / Binder, F. / Buttner, F.H. / Eickmeier, C. / Fiegen, D. / Gross, U. / Grundl, M.A. / Heilker, R. / Hobson, S. / Hoerer, S. / Luippold, A. / Mack, V. / Montel, F. / Peters, ...Authors: Tautermann, C.S. / Binder, F. / Buttner, F.H. / Eickmeier, C. / Fiegen, D. / Gross, U. / Grundl, M.A. / Heilker, R. / Hobson, S. / Hoerer, S. / Luippold, A. / Mack, V. / Montel, F. / Peters, S. / Bhattacharya, S. / Vaidehi, N. / Schnapp, G. / Thamm, S. / Zeeb, M.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5203
Polymers35,2051
Non-polymers3152
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.095, 64.375, 100.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 35204.844 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FWB / 3-[(2~{S})-2-azanylpropyl]-5-(trifluoromethyl)phenol


Mass: 219.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12F3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24 % PEG 3350, 0.2 M ammonium sulfate and 0.1 M BIS-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.655→54.255 Å / Num. obs: 33135 / % possible obs: 79 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.22 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 10.3
Reflection shellResolution: 1.655→1.795 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.195 / Mean I/σ(I) obs: 1.4 / Rsym value: 1.195 / % possible all: 18.5

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Processing

Software
NameVersionClassification
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
Cootmodel building
BUSTER2.11.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BIJ

2bij


Resolution: 1.66→39.69 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.239 985 2.97 %RANDOM
Rwork0.2 ---
obs0.201 33123 79.5 %-
Displacement parametersBiso mean: 25.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.8535 Å20 Å20 Å2
2---2.769 Å20 Å2
3----1.0845 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.66→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 20 377 2735
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082534HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d886SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes439HARMONIC5
X-RAY DIFFRACTIONt_it2534HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion16.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion326SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies14HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3162SEMIHARMONIC4
LS refinement shellResolution: 1.66→1.75 Å / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.2921 -2.81 %
Rwork0.2728 657 -
all0.2732 676 -
obs--11.69 %
Refinement TLS params.Method: refined / Origin x: -14.9433 Å / Origin y: -5.3528 Å / Origin z: 16.5225 Å
111213212223313233
T-0.0183 Å2-0.0016 Å2-0.0007 Å2--0.07 Å2-0.0139 Å2---0.0466 Å2
L0.35 °20.0563 °2-0.314 °2-0.8115 °20.1357 °2--1.4996 °2
S0.006 Å °-0.0213 Å °-0.0156 Å °-0.0133 Å °0.0171 Å °-0.1424 Å °-0.0588 Å °0.1837 Å °-0.0231 Å °
Refinement TLS groupSelection details: { A|* }

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