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Basic information

Entry
Database: PDB / ID: 8jby
TitleVascular endothelial protein tyrosine phosphatase in complex with Cpd-2
ComponentsReceptor-type tyrosine-protein phosphatase beta
KeywordsHYDROLASE / Protein tyrosine phosphatase / FBDD / Inhibitor
Function / homology
Function and homology information


glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / tertiary granule membrane / specific granule membrane / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / tertiary granule membrane / specific granule membrane / dephosphorylation / protein dephosphorylation / protein-tyrosine-phosphatase / angiogenesis / receptor complex / cadherin binding / Neutrophil degranulation / plasma membrane
Similarity search - Function
PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / 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 ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / 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 / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsOrita, T. / Furuzono, T. / Doi, S. / Adachi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2023
Title: Fragment-Based Discovery of Novel VE-PTP Inhibitors Using Orthogonal Biophysical Techniques.
Authors: Asano, W. / Yamanaka, K. / Ohara, Y. / Uhara, T. / Doi, S. / Orita, T. / Iwanaga, T. / Adachi, T. / Fujioka, S. / Akaki, T. / Ikegashira, K. / Hantani, Y.
History
DepositionMay 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase beta
B: Receptor-type tyrosine-protein phosphatase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2588
Polymers68,1132
Non-polymers1,1456
Water5,368298
1
A: Receptor-type tyrosine-protein phosphatase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6915
Polymers34,0561
Non-polymers6354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5673
Polymers34,0561
Non-polymers5112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.692, 123.692, 181.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase beta / Protein-tyrosine phosphatase beta / R-PTP-beta / Vascular endothelial protein tyrosine phosphatase / VE-PTP


Mass: 34056.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB, PTPB / Production host: Escherichia coli (E. coli) / References: UniProt: P23467, protein-tyrosine-phosphatase
#2: Chemical ChemComp-U7L / 4-(hydroxymethyl)-5-(1-methylindol-3-yl)-1,2-oxazole-3-carboxylic acid


Mass: 272.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 100mM HEPES, 9.5%(v/v) PEG 6000, 8.8%(v/v) ethylene glycol, soaking the crystal with 6.25 mM Cpd-2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→92.28 Å / Num. obs: 56401 / % possible obs: 99.5 % / Redundancy: 19.9 % / Biso Wilson estimate: 42.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.016 / Rrim(I) all: 0.072 / Net I/σ(I): 26.1
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 1.216 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3864 / CC1/2: 0.886 / Rpim(I) all: 0.275 / Rrim(I) all: 1.247

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→61.85 Å / SU ML: 0.2473 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 2780 4.93 %
Rwork0.1834 53584 -
obs0.1845 56364 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.36 Å2
Refinement stepCycle: LAST / Resolution: 1.99→61.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4567 0 78 298 4943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264773
X-RAY DIFFRACTIONf_angle_d0.57276481
X-RAY DIFFRACTIONf_chiral_restr0.0441686
X-RAY DIFFRACTIONf_plane_restr0.0042839
X-RAY DIFFRACTIONf_dihedral_angle_d12.96271780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.29521360.30452618X-RAY DIFFRACTION98.85
2.02-2.060.31771410.27522607X-RAY DIFFRACTION98.85
2.06-2.10.31521290.23892601X-RAY DIFFRACTION98.17
2.1-2.140.2551420.22512604X-RAY DIFFRACTION98.99
2.14-2.190.22281350.20212631X-RAY DIFFRACTION99.03
2.19-2.240.22111400.20352659X-RAY DIFFRACTION99.18
2.24-2.30.23881350.19972628X-RAY DIFFRACTION99.28
2.3-2.360.27431240.21162655X-RAY DIFFRACTION99.29
2.36-2.430.24441480.22192650X-RAY DIFFRACTION99.43
2.43-2.510.24031540.22422628X-RAY DIFFRACTION99.5
2.51-2.60.25461330.21272636X-RAY DIFFRACTION98.3
2.6-2.70.25031520.20152663X-RAY DIFFRACTION99.72
2.7-2.820.24431410.18932676X-RAY DIFFRACTION99.61
2.82-2.970.21991430.19242692X-RAY DIFFRACTION99.72
2.97-3.160.22811410.20312690X-RAY DIFFRACTION99.75
3.16-3.40.25111300.18282696X-RAY DIFFRACTION99.02
3.4-3.750.17861580.16652723X-RAY DIFFRACTION100
3.75-4.290.15811270.15382763X-RAY DIFFRACTION99.97
4.29-5.40.1511350.14452783X-RAY DIFFRACTION99.29
5.4-61.850.20581360.19022981X-RAY DIFFRACTION99.49
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)
15.34242950971.375899200631.421948744827.93192819984-2.720804792696.980978611650.158610573695-0.6679534103230.530725457486-0.00718063688228-0.16342742963-0.199972957879-0.6705021435840.5723031316630.03461954166340.297212777258-0.07774491625720.02208555616680.572702339213-0.07903954579580.47431532545640.249489599885.3161591434-5.93386357817
24.458723983241.53538954513-0.774748151536.51617541213-0.677343876594.022575916040.0494100417309-0.327509177198-0.8113052744980.452490121399-0.220388569076-0.4602599343270.649221932607-0.005425535628130.179046314260.306009078371-0.0409090889252-0.01427481503170.426444683191-0.01938048957810.37252271082733.748229379953.47147490043.63540216866
34.547097213461.07749698929-0.4924748373594.742158441430.05964076702574.061486200070.0869787904359-0.217489868691-0.0358199866190.526758163934-0.05801096175820.4692689671140.213013374653-0.354543581167-0.0772340219760.369478145167-0.1032673575840.08549653725410.478208374278-0.07276235270320.33642111954419.847983661761.909371094210.9595553025
42.664365167480.510812053682-1.191091597642.830190497670.3425074686583.354536161690.173939332196-0.3516109753550.1493688696880.435474831147-0.1212631932010.284680299028-0.00429841150869-0.0606222392909-0.06129640990660.376898981958-0.0714370233910.03795095673210.515112406468-0.1121098399640.37848828210425.901056534572.62420413499.50442472381
57.474926632540.6847203633130.6610622391744.124457371494.493620566845.101610817180.1882376392120.05139710087780.890019949331-0.7303176993-0.4555205091170.614784183019-0.988365066868-0.450372491310.2222673516020.4954733012620.01335380020460.02654173951160.427187108982-0.06069747213610.44262815863430.668722454287.44390646720.956866678122
67.2013121066-2.574495052642.864950940519.71274779511-6.800126565834.923140233220.17330066463-0.485677166822-0.4283271266310.892482368188-0.760597259983-0.640187093120.2784172486760.9919677550280.9754484881421.215188865920.241953465235-0.1960978672120.8125378106310.1101371017160.88812067733619.730523057517.653748918215.5691211247
74.448434133751.45082990834-0.9430714610678.18835652261.152384902054.95650555060.06800904297370.0738157009827-0.0549226681594-0.4763992789390.129527817252-0.311198554276-0.1177852588190.324949419509-0.1151674296390.233546168449-0.05008272296910.02713157700750.429571622158-0.04957349332320.30839246827318.366740578441.8976927136-5.92919954751
85.03721747953-0.148079736256-0.1307999840842.950801731920.3271623644032.746705620250.127074022191-0.3054042813550.1438386030320.233971764052-0.03639846314650.1405554404640.0201638378463-0.161233246908-0.06255127131240.266331742144-0.0466326871982-0.007535290005510.3414675922770.03025168996940.308338069431-0.1098740026542.3591436798-0.810465152166
94.62373946784-0.8378068768911.174318492523.098449107620.4165792771284.407811834310.151536560491-0.339062246219-0.4792443490180.297431060324-0.106841149840.2825725789450.411958070709-0.149735409531-0.004383168564260.273860531469-0.1096400402450.07583843031840.4163551088020.09712042617420.418359965345-2.9504239296334.38269851983.31421108037
102.83713582707-0.3082533944420.1063805541958.18581235473-0.8931633411325.365148775180.163689413909-0.221694781088-0.7430274286990.01680588312720.04733026407890.09329835044010.931226468172-0.0629558921335-0.1366473989830.386124434329-0.0185915162478-0.01581531950430.376166811340.117974184280.4494644767633.5371875623428.17883184240.941146938924
115.283021820592.24104955049-2.145148931274.4792390736-1.484378605785.34558224698-0.0492740712328-0.501099593721-1.018079016880.4864074422540.0281468789233-0.4010296571750.9540004474740.02443284359770.1239387618930.710299772330.0848646299742-0.1289573803560.4827327398930.1973622401660.68291070113810.640782755921.80136314087.66719769524
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1685 through 1710 )AA1685 - 17101 - 26
22chain 'A' and (resid 1711 through 1763 )AA1711 - 176327 - 79
33chain 'A' and (resid 1764 through 1837 )AA1764 - 183780 - 153
44chain 'A' and (resid 1838 through 1949 )AA1838 - 1949154 - 265
55chain 'A' and (resid 1950 through 1971 )AA1950 - 1971266 - 287
66chain 'B' and (resid 1694 through 1709 )BF1694 - 17091 - 16
77chain 'B' and (resid 1710 through 1759 )BF1710 - 175917 - 63
88chain 'B' and (resid 1760 through 1850 )BF1760 - 185064 - 154
99chain 'B' and (resid 1851 through 1892 )BF1851 - 1892155 - 196
1010chain 'B' and (resid 1893 through 1926 )BF1893 - 1926197 - 230
1111chain 'B' and (resid 1927 through 1968 )BF1927 - 1968231 - 272

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