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- PDB-5ura: Enantiomer-Specific Binding of the Potent Antinociceptive Agent S... -

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Basic information

Entry
Database: PDB / ID: 5ura
TitleEnantiomer-Specific Binding of the Potent Antinociceptive Agent SBFI-26 to Anandamide transporters FABP7
ComponentsFatty acid-binding protein, brain
KeywordsLIPID BINDING PROTEIN/INHIBITOR / inhibitor / LIPID BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


NOTCH3 Intracellular Domain Regulates Transcription / Triglyceride catabolism / fatty acid transport / epithelial cell proliferation / fatty acid binding / nervous system development / negative regulation of cell population proliferation / lipid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-8KS / Fatty acid-binding protein, brain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85002167328 Å
AuthorsHsu, H.-C. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA035924 United States
CitationJournal: Biochemistry / Year: 2017
Title: The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites.
Authors: Hsu, H.C. / Tong, S. / Zhou, Y. / Elmes, M.W. / Yan, S. / Kaczocha, M. / Deutsch, D.G. / Rizzo, R.C. / Ojima, I. / Li, H.
History
DepositionFeb 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, brain
B: Fatty acid-binding protein, brain
C: Fatty acid-binding protein, brain
D: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,21916
Polymers60,7614
Non-polymers2,45812
Water10,431579
1
A: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8054
Polymers15,1901
Non-polymers6153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8054
Polymers15,1901
Non-polymers6153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8054
Polymers15,1901
Non-polymers6153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid-binding protein, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8054
Polymers15,1901
Non-polymers6153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.840, 73.330, 70.530
Angle α, β, γ (deg.)90.000, 92.980, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
DetailsMonomer as determined by gel filtration

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Components

#1: Protein
Fatty acid-binding protein, brain / Brain lipid-binding protein / BLBP / Brain-type fatty acid-binding protein / B-FABP / Fatty acid- ...Brain lipid-binding protein / BLBP / Brain-type fatty acid-binding protein / B-FABP / Fatty acid-binding protein 7 / Mammary-derived growth inhibitor related


Mass: 15190.174 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP7, BLBP, FABPB, MRG / Production host: Escherichia coli (E. coli) / References: UniProt: O15540
#2: Chemical
ChemComp-8KS / (1S,2S,3S,4S)-3-{[(naphthalen-1-yl)oxy]carbonyl}-2,4-diphenylcyclobutane-1-carboxylic acid


Mass: 422.472 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H22O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH8.5, 0.1 M lithium sulfate, and 33% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→53.77 Å / Num. all: 174183 / Num. obs: 46797 / Biso Wilson estimate: 21.2914842067 Å2 / Rmerge(I) obs: 0.107
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6795 / CC1/2: 0.636 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FDQ

1fdq


Resolution: 1.85002167328→36.2521887721 Å / SU ML: 0.221034257719 / Cross valid method: FREE R-VALUE / σ(F): 1.35214011819 / Phase error: 22.3950668524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206216163601 2334 4.99176593879 %
Rwork0.179526537214 44423 -
obs0.180937689518 46757 99.8228010248 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.9522072011 Å2
Refinement stepCycle: LAST / Resolution: 1.85002167328→36.2521887721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 168 579 4995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003896854996914492
X-RAY DIFFRACTIONf_angle_d0.6750998392066069
X-RAY DIFFRACTIONf_chiral_restr0.0486404774227680
X-RAY DIFFRACTIONf_plane_restr0.00318993702471761
X-RAY DIFFRACTIONf_dihedral_angle_d19.76000922722593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88780.3341266153531440.3012247674522578X-RAY DIFFRACTION100
1.8878-1.92880.3174590909721300.2659530929922621X-RAY DIFFRACTION100
1.9288-1.97370.249324192481240.247427969272607X-RAY DIFFRACTION100
1.9737-2.0230.2834101431781210.2305808166692640X-RAY DIFFRACTION100
2.023-2.07770.2787805592161300.2297400690232608X-RAY DIFFRACTION100
2.0777-2.13890.2449821994261310.2251543041382604X-RAY DIFFRACTION100
2.1389-2.20790.2563931808441550.207375828982603X-RAY DIFFRACTION100
2.2079-2.28680.2378892478731160.2060612889732611X-RAY DIFFRACTION100
2.2868-2.37830.2621606427181330.1985624459032598X-RAY DIFFRACTION100
2.3783-2.48660.267067373231230.1935414200372630X-RAY DIFFRACTION99.9274047187
2.4866-2.61760.2687707491951300.1856586307762651X-RAY DIFFRACTION100
2.6176-2.78160.2141253354631090.1834553083912617X-RAY DIFFRACTION100
2.7816-2.99620.21917660881330.1808809286252645X-RAY DIFFRACTION100
2.9962-3.29760.1919634046661600.1656396265012582X-RAY DIFFRACTION99.9271137026
3.2976-3.77430.1614507036591560.1395761449362641X-RAY DIFFRACTION100
3.7743-4.75360.1205886699361550.1290192187942604X-RAY DIFFRACTION100
4.7536-36.25910.1871157396411840.1554420997162583X-RAY DIFFRACTION97.2241742797

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