[English] 日本語
Yorodumi
- PDB-9yg2: Targeting PTPN22 at non-orthosteric binding sites - a fragment ap... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yg2
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
: / Tyrosine-protein phosphatase non-receptor type 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 22
B: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,37014
Polymers75,5102
Non-polymers86012
Water3,675204
1
A: Tyrosine-protein phosphatase non-receptor type 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,43710
Polymers37,7551
Non-polymers6819
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)37,9344
Polymers37,7551
Non-polymers1783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.500, 48.380, 120.160
Angle α, β, γ (deg.)90.00, 102.74, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#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: 37755.070 Da / Num. of mol.: 2
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

-
Non-polymers , 6 types, 216 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-A1CWK / 5-chloro-3-methyl-1-[(3R)-pyrrolidin-3-yl]-1H-indole


Mass: 234.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15ClN2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: PTPN22-PD303 (20mg/ml), PEGII C9: 0.1 M TRIS pH 8.5, 0.2 M MgCl2, & 16 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→48.58 Å / Num. obs: 32215 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Χ2: 0.98 / Net I/σ(I): 16.4 / Num. measured all: 208441
Reflection shellResolution: 2.26→2.33 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.807 / Num. measured all: 18792 / Num. unique obs: 2958 / CC1/2: 0.803 / Rpim(I) all: 0.346 / Rrim(I) all: 0.88 / Χ2: 0.87 / Net I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→48.58 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2423 1718 5.34 %
Rwork0.1895 --
obs0.1922 32197 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 52 204 5242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025186
X-RAY DIFFRACTIONf_angle_d0.4786995
X-RAY DIFFRACTIONf_dihedral_angle_d5.176689
X-RAY DIFFRACTIONf_chiral_restr0.041748
X-RAY DIFFRACTIONf_plane_restr0.003882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.330.30631410.24962535X-RAY DIFFRACTION100
2.33-2.40.28731540.23382483X-RAY DIFFRACTION100
2.4-2.490.27691590.23322483X-RAY DIFFRACTION100
2.49-2.590.27561550.232516X-RAY DIFFRACTION100
2.59-2.70.28111330.21762541X-RAY DIFFRACTION100
2.7-2.850.32471280.22142542X-RAY DIFFRACTION100
2.85-3.030.29391300.2252559X-RAY DIFFRACTION100
3.03-3.260.28481320.21322518X-RAY DIFFRACTION100
3.26-3.590.23061400.18752536X-RAY DIFFRACTION100
3.59-4.110.22911550.16732545X-RAY DIFFRACTION100
4.11-5.170.18491540.14982562X-RAY DIFFRACTION100
5.17-48.580.23621370.18072659X-RAY DIFFRACTION100
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)
12.35110.1475-0.49686.0964-0.9322.6594-0.0924-0.77010.27230.8616-0.09540.03970.0006-0.23110.00870.6437-0.06490.08520.7274-0.1090.57673.144914.30871.3771
25.2885-1.5163-1.44672.90560.35662.593-0.33720.12490.026-0.19220.0938-0.4164-0.00920.19410.13550.5772-0.0742-0.00440.416-0.01980.566917.118419.547752.3268
32.8565-0.50780.97442.05940.26466.58350.13680.33180.3222-0.15690.1070.1018-0.36051.0554-0.27170.3952-0.02650.05740.53480.0140.449824.12193.847436.4894
42.85671.21251.14540.56260.59772.9228-0.07510.10860.121-0.2045-0.0023-0.03640.0140.07710.07080.46130.03260.03250.39460.02820.42917.63972.183839.017
51.85550.2949-0.24270.845-0.18271.5064-0.06510.2564-0.2161-0.07810.054-0.0230.22180.39040.01490.44970.03080.01230.36570.00520.414211.6625-5.815339.0114
63.6551-1.28430.27393.1424-0.00973.0944-0.24690.61030.31340.1317-0.04110.3593-0.3735-0.4360.36940.4396-0.0632-0.08590.48760.05010.48410.75912.985538.1771
73.8165-0.36540.43212.54911.0363.18420.11530.389-0.1086-0.1342-0.19380.51070.3471-0.35990.10610.4523-0.0406-0.05130.5146-0.060.4956-4.6821-6.43832.9321
84.0365-0.39040.16072.15482.1955.0005-0.0246-0.00670.19890.054-0.18120.3959-0.09-0.44070.1230.3457-0.08490.03780.37230.02360.3814-2.5359-0.704146.4154
92.57740.7508-0.48673.2391-0.19223.6974-0.0671-0.5213-0.16790.1828-0.156-0.17950.4225-0.10030.2780.383-0.03290.02260.4234-0.00230.38955.7374.204759.8362
100.7553-0.636-0.29241.56150.92820.59140.1294-0.04410.0934-0.2203-0.2011-0.0370.0892-0.05180.0920.4362-0.00670.03410.3129-0.03420.416813.76719.698951.4762
113.52721.0707-0.56373.4385-1.46625.1730.227-0.62540.28920.6322-0.02240.6148-0.3398-0.6862-0.07750.4583-0.02430.03160.5378-0.06710.4696-1.104310.498562.5731
121.5758-0.8438-1.54992.89751.16141.9542-0.12520.1072-0.2354-0.0751-0.00390.23770.3084-0.34070.06960.5162-0.048-0.08470.5714-0.07340.415-34.6818-11.04545.5941
132.4725-0.1221-0.83051.09350.1233.2329-0.05780.30290.3308-0.176-0.0786-0.5308-0.09850.77840.08710.4521-0.06250.03020.6350.10440.6031-10.89616.96243.1673
142.7298-0.38561.12881.55430.37883.6584-0.1128-0.07510.44050.2981-0.0295-0.4588-0.27010.70160.13710.43-0.09-0.12410.4970.04580.5079-10.90059.229421.0384
155.34790.91740.40952.0093-0.0994.8752-0.1927-0.1717-0.06340.32580.0132-0.11140.07620.13990.10480.37860.035-0.03530.3767-0.03930.3765-22.37246.199621.9792
163.23220.0038-1.40562.4030.74462.78080.10560.17940.1595-0.2306-0.0913-0.0226-0.0946-0.2152-0.02280.34830.0183-0.00080.3489-0.00710.275-29.5264-0.6698.0972
173.4887-0.7719-2.07561.50461.06013.40060.0987-0.02810.0220.2057-0.15980.06740.1889-0.5506-0.01240.4105-0.0457-0.01080.45420.01840.356-39.8107-3.870417.2264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 137 )
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 165 )
8X-RAY DIFFRACTION8chain 'A' and (resid 166 through 231 )
9X-RAY DIFFRACTION9chain 'A' and (resid 232 through 257 )
10X-RAY DIFFRACTION10chain 'A' and (resid 258 through 275 )
11X-RAY DIFFRACTION11chain 'A' and (resid 276 through 300 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 40 )
13X-RAY DIFFRACTION13chain 'B' and (resid 41 through 98 )
14X-RAY DIFFRACTION14chain 'B' and (resid 99 through 165 )
15X-RAY DIFFRACTION15chain 'B' and (resid 166 through 231 )
16X-RAY DIFFRACTION16chain 'B' and (resid 232 through 275 )
17X-RAY DIFFRACTION17chain 'B' and (resid 276 through 303 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more