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- PDB-8u5m: Structure of Sts-1 HP domain with rebamipide -

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Basic information

Entry
Database: PDB / ID: 8u5m
TitleStructure of Sts-1 HP domain with rebamipide
ComponentsUbiquitin-associated and SH3 domain-containing protein B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Sts-1 / histidine phosphatase / inhibitor / UBASH3B / TULA-2 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding ...regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding / platelet aggregation / ubiquitin protein ligase binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
UBASH3B, SH3 domain / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily ...UBASH3B, SH3 domain / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
: / Ubiquitin-associated and SH3 domain-containing protein B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsAzia, F. / Dey, R. / French, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI141592 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Rebamipide and Derivatives are Potent, Selective Inhibitors of Histidine Phosphatase Activity of the Suppressor of T Cell Receptor Signaling Proteins.
Authors: Aziz, F. / Reddy, K. / Fernandez Vega, V. / Dey, R. / Hicks, K.A. / Rao, S. / Jordan, L.O. / Smith, E. / Shumate, J. / Scampavia, L. / Carpino, N. / Spicer, T.P. / French, J.B.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-associated and SH3 domain-containing protein B
B: Ubiquitin-associated and SH3 domain-containing protein B
C: Ubiquitin-associated and SH3 domain-containing protein B
D: Ubiquitin-associated and SH3 domain-containing protein B
E: Ubiquitin-associated and SH3 domain-containing protein B
F: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,6999
Polymers192,5876
Non-polymers1,1123
Water3,261181
1
A: Ubiquitin-associated and SH3 domain-containing protein B
F: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5663
Polymers64,1962
Non-polymers3711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-23 kcal/mol
Surface area21360 Å2
MethodPISA
2
B: Ubiquitin-associated and SH3 domain-containing protein B
E: Ubiquitin-associated and SH3 domain-containing protein B


Theoretical massNumber of molelcules
Total (without water)64,1962
Polymers64,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-24 kcal/mol
Surface area21510 Å2
MethodPISA
3
C: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules

D: Ubiquitin-associated and SH3 domain-containing protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9374
Polymers64,1962
Non-polymers7422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2980 Å2
ΔGint-23 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.650, 122.274, 99.588
Angle α, β, γ (deg.)90.00, 112.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ubiquitin-associated and SH3 domain-containing protein B


Mass: 32097.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBASH3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TF42
#2: Chemical ChemComp-VJX / Rebamipide / N-(4-chlorobenzoyl)-3-(2-oxo-1,2-dihydroquinolin-4-yl)-L-alanine


Mass: 370.786 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H15ClN2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 Hepes 10% ethylene glycol 0.3 M magnesium chloride 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.46→122.27 Å / Num. obs: 65248 / % possible obs: 98.3 % / Redundancy: 2.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.06 / Rrim(I) all: 0.103 / Net I/σ(I): 10 / Num. measured all: 178798
Reflection shellResolution: 2.46→2.52 Å / % possible obs: 98.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.824 / Num. measured all: 12714 / Num. unique obs: 4601 / CC1/2: 0.483 / Rpim(I) all: 0.591 / Rrim(I) all: 1.019 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VR6

5vr6


Resolution: 2.46→73.55 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.913 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27448 3230 5 %RANDOM
Rwork0.229 ---
obs0.23119 61989 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.922 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å2-0 Å2-0.44 Å2
2--0.35 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: 1 / Resolution: 2.46→73.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11477 0 78 181 11736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01311852
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710474
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.64416200
X-RAY DIFFRACTIONr_angle_other_deg1.111.56624193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49951536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29521.949513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.464151704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2471561
X-RAY DIFFRACTIONr_chiral_restr0.040.21614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022479
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8256.4246160
X-RAY DIFFRACTIONr_mcbond_other1.8246.4246158
X-RAY DIFFRACTIONr_mcangle_it3.1529.6297688
X-RAY DIFFRACTIONr_mcangle_other3.1529.6297688
X-RAY DIFFRACTIONr_scbond_it1.446.2615692
X-RAY DIFFRACTIONr_scbond_other1.446.2615693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4799.3878513
X-RAY DIFFRACTIONr_long_range_B_refined4.99773.68312793
X-RAY DIFFRACTIONr_long_range_B_other4.99473.68312791
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 250 -
Rwork0.323 4573 -
obs--98.91 %

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