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- PDB-2h04: Structural studies of protein tyrosine phosphatase beta catalytic... -

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Basic information

Entry
Database: PDB / ID: 2h04
TitleStructural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors
ComponentsProtein tyrosine phosphatase, receptor type, B,
KeywordsHYDROLASE / protein tyrosine phosphatase / WPD-loop / sulfamic acid / phosphatase / inhibitor / drug design
Function / homology
Function and homology information


glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / protein dephosphorylation / specific granule membrane / protein-tyrosine-phosphatase / osteoblast differentiation / angiogenesis ...glial cell migration / transmembrane receptor protein tyrosine phosphatase activity / phosphate-containing compound metabolic process / dephosphorylation / tertiary granule membrane / protein dephosphorylation / specific granule membrane / protein-tyrosine-phosphatase / osteoblast differentiation / 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 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 ...PTPRJ, transmembrane domain / TM proximal of protein tyrosine phosphatase, receptor type J / : / 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 profile. / Tyrosine-specific protein phosphatases domain / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-4UN / Receptor-type tyrosine-protein phosphatase beta / Receptor-type tyrosine-protein phosphatase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEvdokimov, A.G. / Pokross, M.E. / Walter, R.L. / Mekel, M. / Gray, J.L. / Peters, K.G. / Maier, M.B. / Amarasinghe, K.D. / Clark, C.M. / Nichols, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Design and synthesis of potent, non-peptidic inhibitors of HPTPbeta.
Authors: Amarasinghe, K.K. / Evdokimov, A.G. / Xu, K. / Clark, C.M. / Maier, M.B. / Srivastava, A. / Colson, A.O. / Gerwe, G.S. / Stake, G.E. / Howard, B.W. / Pokross, M.E. / Gray, J.L. / Peters, K.G.
History
DepositionMay 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine phosphatase, receptor type, B,
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7442
Polymers36,2881
Non-polymers4551
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.803, 70.120, 90.722
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 Protein tyrosine phosphatase, receptor type, B,


Mass: 36288.035 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 1662-1973
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRB / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10
References: UniProt: Q3MIV7, UniProt: P23467*PLUS, protein-tyrosine-phosphatase
#2: Chemical ChemComp-4UN / {4-[2,2-BIS(5-METHYL-1,2,4-OXADIAZOL-3-YL)-3-PHENYLPROPYL]PHENYL}SULFAMIC ACID


Mass: 455.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N5O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, pH 8.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→34.86 Å / Num. all: 13248 / Num. obs: 13248 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.88
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.83 / Num. unique all: 1529 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPM (WITH MODIFICATIONS)

1rpm


Resolution: 2.3→34.86 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.831 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.381 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.238 649 4.9 %RANDOM
Rwork0.169 ---
all0.172 13207 --
obs0.17 13207 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.455 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 32 141 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212391
X-RAY DIFFRACTIONr_angle_refined_deg2.1551.9553246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3475281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52523.496123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.27815406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3911520
X-RAY DIFFRACTIONr_chiral_restr0.1450.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021843
X-RAY DIFFRACTIONr_nbd_refined0.2220.21078
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21589
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3290.219
X-RAY DIFFRACTIONr_mcbond_it1.7021.51425
X-RAY DIFFRACTIONr_mcangle_it2.79322276
X-RAY DIFFRACTIONr_scbond_it4.61331090
X-RAY DIFFRACTIONr_scangle_it6.4634.5968
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 49 -
Rwork0.175 899 -
obs-948 97.83 %

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