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- PDB-9yg0: Targeting PTPN22 at non-orthosteric binding sites - a fragment ap... -

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Basic information

Entry
Database: PDB / ID: 9yg0
TitleTargeting PTPN22 at non-orthosteric binding sites - a fragment approach
ComponentsTyrosine-protein phosphatase non-receptor type 22
KeywordsIMMUNE SYSTEM / non-receptor protein tyrosine phosphatase
Function / homology
Function and homology information


phosphoanandamide dephosphorylation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of JUN kinase activity / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of protein K63-linked ubiquitination ...phosphoanandamide dephosphorylation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of B cell receptor signaling pathway / regulation of natural killer cell proliferation / positive regulation of toll-like receptor 3 signaling pathway / negative regulation of JUN kinase activity / regulation of non-canonical NF-kappaB signal transduction / negative regulation of p38MAPK cascade / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / negative regulation of T cell activation / negative regulation of interleukin-8 production / negative regulation of T cell receptor signaling pathway / regulation of innate immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of NLRP3 inflammasome complex assembly / phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / negative regulation of interleukin-6 production / T cell differentiation / negative regulation of tumor necrosis factor production / positive regulation of type I interferon production / protein-tyrosine-phosphatase / negative regulation of autophagy / protein tyrosine phosphatase activity / lipopolysaccharide-mediated signaling pathway / SH3 domain binding / autophagy / lipid metabolic process / cytoplasmic side of plasma membrane / kinase binding / positive regulation of type II interferon production / T cell receptor signaling pathway / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / negative regulation of gene expression / ubiquitin protein ligase binding / positive regulation of gene expression / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Non-receptor tyrosine-protein phosphatase 22 / : / : / 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. ...Non-receptor tyrosine-protein phosphatase 22 / : / : / 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
: / ETHANOL / Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDi Lello, P. / Wells, M.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Omega / Year: 2026
Title: Targeting PTPN22 at Nonorthosteric Binding Sites - A Fragment Approach
Authors: Di Lello, P. / Wells, M.M. / Davis, B. / Daniels, Z. / Garner, T.P. / Gazzard, L. / Harris, R. / Hubbard, R.E. / Landry, M.L. / Martin, B. / Morgan, J.L.W. / Patapoff, A. / Simmonite, H. / ...Authors: Di Lello, P. / Wells, M.M. / Davis, B. / Daniels, Z. / Garner, T.P. / Gazzard, L. / Harris, R. / Hubbard, R.E. / Landry, M.L. / Martin, B. / Morgan, J.L.W. / Patapoff, A. / Simmonite, H. / Skelton, N. / Ultsch, M. / Walters, B.T. / Wu, P. / Dimitrova, Y.N. / Huard, K.
History
DepositionSep 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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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 22
B: Tyrosine-protein phosphatase non-receptor type 22
C: Tyrosine-protein phosphatase non-receptor type 22
D: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,29322
Polymers151,5454
Non-polymers1,74818
Water13,367742
1
A: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3155
Polymers37,8861
Non-polymers4294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3187
Polymers37,8861
Non-polymers4316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3195
Polymers37,8861
Non-polymers4334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3415
Polymers37,8861
Non-polymers4554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.023, 48.395, 120.139
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Tyrosine-protein phosphatase non-receptor type 22 / Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain ...Hematopoietic cell protein-tyrosine phosphatase 70Z-PEP / Lymphoid phosphatase / LyP / PEST-domain phosphatase / PEP


Mass: 37886.266 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN22, PTPN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2R2, protein-tyrosine-phosphatase

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Non-polymers , 6 types, 760 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-A1CWM / 1-[(3S)-3-amino-2,3-dihydro-1H-indol-1-yl]-3-phenylpropan-1-one


Mass: 266.338 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18N2O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: PEGII C9: 0.1 M TRIS pH 8.5, 0.2 M magnesium chloride, & 16 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1806 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 1.76→58.61 Å / Num. obs: 101453 / % possible obs: 99.3 % / Redundancy: 4 % / CC1/2: 0.999 / Net I/σ(I): 14.9
Reflection shellResolution: 1.76→1.823 Å / Num. unique obs: 5074 / CC1/2: 0.853

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487-000)refinement
autoPROCdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→58.61 Å / Cross valid method: FREE R-VALUE / σ(F): 46.04 / Phase error: 42.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2401 5134 5.06 %
Rwork0.2093 --
obs0.2112 101434 75.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→58.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9831 0 119 742 10692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310180
X-RAY DIFFRACTIONf_angle_d0.48913764
X-RAY DIFFRACTIONf_dihedral_angle_d5.8911371
X-RAY DIFFRACTIONf_chiral_restr0.0411484
X-RAY DIFFRACTIONf_plane_restr0.0021739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.790.3885160.3575363X-RAY DIFFRACTION
1.79-1.820.3026451095X-RAY DIFFRACTION
1.82-1.860.33121072130X-RAY DIFFRACTION32
1.86-1.890.600350.499883X-RAY DIFFRACTION
1.89-1.930.40912140.3613644X-RAY DIFFRACTION54
1.96-1.980.29391160.28992228X-RAY DIFFRACTION34
1.98-2.030.29073370.26676404X-RAY DIFFRACTION95
2.03-2.090.31533890.29226208X-RAY DIFFRACTION93
2.09-2.150.26242910.23646341X-RAY DIFFRACTION95
2.15-2.220.24313180.22936401X-RAY DIFFRACTION95
2.22-2.290.28213540.24996261X-RAY DIFFRACTION93
2.29-2.390.25453430.22166341X-RAY DIFFRACTION95
2.39-2.50.24512770.2256442X-RAY DIFFRACTION96
2.5-2.630.24042940.22136411X-RAY DIFFRACTION95
2.63-2.790.21052150.22223823X-RAY DIFFRACTION57
2.79-3.010.24653370.20436424X-RAY DIFFRACTION95
3.01-3.310.23563140.20596394X-RAY DIFFRACTION95
3.31-3.790.23053190.18766386X-RAY DIFFRACTION94
3.79-4.770.1873380.15126424X-RAY DIFFRACTION94
4.77-80.24043560.20776646X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1535-0.1618-0.01981.0252-0.65821.90060.02440.0882-0.005-0.0668-0.0614-0.07870.0880.1740.03010.15070.01890.00760.1317-0.00780.1528-48.940925.930511.0992
20.764-0.0165-0.12420.94110.55241.99070.0397-0.06880.03270.0898-0.09230.0880.0904-0.17220.05190.1381-0.02570.01280.1990.00930.1585-11.02181.8665-11.2021
31.86420.1291-0.12890.89150.22041.3853-0.0471-0.04280.10660.01840.0102-0.08620.01650.09330.03780.14480.0225-0.01550.12150.00530.1397-38.6311.6022-45.1067
41.8441-0.0621-0.06440.84660.14661.0484-0.03980.07050.10460.01190.0302-0.09160.0007-0.0290.00850.14410.0026-0.00640.1794-0.00890.125421.31421.4883-45.1211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 299)
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 299)
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 303)
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 303)

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