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- PDB-9eez: STEP (PTPN5) with active-site disulfide bond and covalent ligand ... -

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Basic information

Entry
Database: PDB / ID: 9eez
TitleSTEP (PTPN5) with active-site disulfide bond and covalent ligand bound to distal C505 and C518
ComponentsTyrosine-protein phosphatase non-receptor type 5
KeywordsHYDROLASE / STEP / PTPN5 / allostery / disulfide / covalent ligand
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, 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 ...Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like
Similarity search - Domain/homology
: / Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGuerrero, L. / Ebrahim, A. / Riley, B.T. / Keedy, D.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133769 United States
Citation
Journal: Proteins / Year: 2025
Title: Three STEPs Forward: A Trio of Unexpected Structures of PTPN5.
Authors: Guerrero, L. / Ebrahim, A. / Riley, B.T. / Kim, S.H. / Bishop, A.C. / Wu, J. / Han, Y.N. / Tautz, L. / Keedy, D.A.
#1: Journal: Biorxiv / Year: 2025
Title: Three STEPs forward: A trio of unexpected structures of PTPN5.
Authors: Guerrero, L. / Ebrahim, A. / Riley, B.T. / Kim, S.H. / Bishop, A.C. / Wu, J. / Han, Y.N. / Tautz, L. / Keedy, D.A.
History
DepositionNov 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author / Item: _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 7, 2025Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Feb 4, 2026Group: Database references / Category: citation / citation_author

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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)36,0216
Polymers35,2051
Non-polymers8165
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.144, 64.194, 137.182
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 BL21(DE3) (bacteria) / References: UniProt: P54829, protein-tyrosine-phosphatase
#2: Chemical ChemComp-A1BHT / [4-(bromoacetyl)phenoxy]acetic acid


Mass: 273.080 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9BrO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 3350, 0.2 M lithium sulfate, 0.1 M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.6→64.2 Å / Num. obs: 47763 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 24.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 13.2
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 2.8 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2270 / CC1/2: 0.406 / Rpim(I) all: 0.82 / Rrim(I) all: 2.922

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia23.7.1data reduction
DIALS3.7.1-gfb34cbf01-releasedata scaling
PHASER2.8.2 (syn 8393)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.87 Å / SU ML: 0.2407 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.5279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 2336 4.9 %
Rwork0.2017 45291 -
obs0.2033 47627 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 42 159 2386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01482329
X-RAY DIFFRACTIONf_angle_d1.18783170
X-RAY DIFFRACTIONf_chiral_restr0.0783340
X-RAY DIFFRACTIONf_plane_restr0.0105412
X-RAY DIFFRACTIONf_dihedral_angle_d13.9744879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.3791390.38212564X-RAY DIFFRACTION98.65
1.63-1.670.34171600.32682583X-RAY DIFFRACTION99.6
1.67-1.710.29731430.29772621X-RAY DIFFRACTION99.78
1.71-1.750.25061120.27292664X-RAY DIFFRACTION99.68
1.75-1.80.30231430.26752606X-RAY DIFFRACTION99.82
1.8-1.850.28081290.26322640X-RAY DIFFRACTION99.86
1.85-1.910.3241350.26592661X-RAY DIFFRACTION99.82
1.91-1.980.27891410.24292614X-RAY DIFFRACTION99.86
1.98-2.060.26251380.21142634X-RAY DIFFRACTION99.75
2.06-2.150.23581510.20922651X-RAY DIFFRACTION99.86
2.15-2.260.24671270.20792644X-RAY DIFFRACTION99.64
2.26-2.410.26411420.20872674X-RAY DIFFRACTION99.86
2.41-2.590.2241330.19632665X-RAY DIFFRACTION99.89
2.59-2.850.23291470.19692707X-RAY DIFFRACTION99.89
2.85-3.260.21251360.19912699X-RAY DIFFRACTION100
3.26-4.110.22371230.16852764X-RAY DIFFRACTION100
4.11-46.870.20351370.1832900X-RAY DIFFRACTION99.93

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