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- PDB-5ur9: Enantiomer-Specific Binding of the Potent Antinociceptive Agent S... -

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Basic information

Entry
Database: PDB / ID: 5ur9
TitleEnantiomer-Specific Binding of the Potent Antinociceptive Agent SBFI-26 to Anandamide transporters FABP5
ComponentsFatty acid-binding protein, epidermal
KeywordsLIPID BINDING PROTEIN/INHIBITOR / inhibitor / LIPID BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / fatty acid transport / long-chain fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / synapse / lipid binding / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / MYRISTIC ACID / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19800343737 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: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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, epidermal
B: Fatty acid-binding protein, epidermal
C: Fatty acid-binding protein, epidermal
D: Fatty acid-binding protein, epidermal
E: Fatty acid-binding protein, epidermal
F: Fatty acid-binding protein, epidermal
G: Fatty acid-binding protein, epidermal
H: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,95337
Polymers123,7428
Non-polymers6,21129
Water6,197344
1
A: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4076
Polymers15,4681
Non-polymers9395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3115
Polymers15,4681
Non-polymers8434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3115
Polymers15,4681
Non-polymers8434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3115
Polymers15,4681
Non-polymers8434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0824
Polymers15,4681
Non-polymers6153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9863
Polymers15,4681
Non-polymers5192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3215
Polymers15,4681
Non-polymers8534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Fatty acid-binding protein, epidermal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2254
Polymers15,4681
Non-polymers7573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.990, 78.110, 78.830
Angle α, β, γ (deg.)61.660, 69.610, 78.010
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
DetailsMonomer as determined by gel filtration

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Fatty acid-binding protein, epidermal / Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein 5 / Psoriasis- ...Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein 5 / Psoriasis-associated fatty acid-binding protein homolog / PA-FABP


Mass: 15467.732 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01469

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Non-polymers , 5 types, 373 molecules

#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.: 8 / Source method: obtained synthetically / Formula: C28H22O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 2% polyethylene glycol 400, and 2.1 M ammonium sulfate 15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.198→54.94 Å / Num. obs: 63855 / % possible obs: 92.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 35.668891815 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.2
Reflection shellResolution: 2.198→2.32 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8986 / CC1/2: 0.787 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LKP

4lkp


Resolution: 2.19800343737→40.7600279886 Å / SU ML: 0.290867111957 / Cross valid method: FREE R-VALUE / σ(F): 1.97336789233 / Phase error: 25.892558969
RfactorNum. reflection% reflection
Rfree0.236864061658 3231 5.06156593665 %
Rwork0.196655333535 --
obs0.198676383641 63834 92.4701587669 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.2183468876 Å2
Refinement stepCycle: LAST / Resolution: 2.19800343737→40.7600279886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8466 0 427 344 9237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007972350018328997
X-RAY DIFFRACTIONf_angle_d0.96925476444212077
X-RAY DIFFRACTIONf_chiral_restr0.05265834533261371
X-RAY DIFFRACTIONf_plane_restr0.005692385858091490
X-RAY DIFFRACTIONf_dihedral_angle_d15.31857756225336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.198-2.23080.3447067968041260.2836549296412416X-RAY DIFFRACTION83.5359842261
2.2308-2.26570.3406250158571250.2656028863642536X-RAY DIFFRACTION90.4794287657
2.2657-2.30280.3058430183341450.2509962328382682X-RAY DIFFRACTION92.2048271363
2.3028-2.34250.3065854672691360.2440011026812559X-RAY DIFFRACTION91.9481405664
2.3425-2.38510.2773818803081450.2408851803972666X-RAY DIFFRACTION92.0432220039
2.3851-2.4310.2867754462581420.2221871947862621X-RAY DIFFRACTION92.998990239
2.431-2.48060.3003672765651460.2277286232632627X-RAY DIFFRACTION92.8045515395
2.4806-2.53450.2797745575971460.2142123358542659X-RAY DIFFRACTION93.0039787798
2.5345-2.59350.2380321456841590.2125252124872681X-RAY DIFFRACTION93.8532716457
2.5935-2.65830.2589236131021470.2114224719132647X-RAY DIFFRACTION93.1022992336
2.6583-2.73020.3095337336531350.2149321811782651X-RAY DIFFRACTION93.2396251673
2.7302-2.81050.2889693101151450.2177170744642673X-RAY DIFFRACTION93.3112582781
2.8105-2.90120.2645674024961500.2186992485332659X-RAY DIFFRACTION93.6333333333
2.9012-3.00480.2730146007071330.2193324037272665X-RAY DIFFRACTION93.5160427807
3.0048-3.12510.2727600349241480.2172062786982665X-RAY DIFFRACTION93.5483870968
3.1251-3.26730.2637861872591360.2031872131032660X-RAY DIFFRACTION93.3555926544
3.2673-3.43950.2129432334241200.1861610425382673X-RAY DIFFRACTION93.661971831
3.4395-3.65480.2305825649991500.1811631198032669X-RAY DIFFRACTION93.7167553191
3.6548-3.93680.207358328541440.1850088172442655X-RAY DIFFRACTION93.1757656458
3.9368-4.33260.1968728804921490.1686877381662660X-RAY DIFFRACTION93.6957971981
4.3326-4.95860.1626834576771250.1510893617632667X-RAY DIFFRACTION92.9427430093
4.9586-6.24370.1995088266061290.1759872159352662X-RAY DIFFRACTION92.9094540613
6.2437-40.7670.2157096127451500.19828697732550X-RAY DIFFRACTION90.2406417112

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