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- PDB-3p6h: Human adipocyte lipid-binding protein FABP4 in complex with (S)-i... -

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Basic information

Entry
Database: PDB / ID: 3p6h
TitleHuman adipocyte lipid-binding protein FABP4 in complex with (S)-ibuprofen
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / lipocalin / beta barrel / fatty acid binding protein / drug / nonsteroidal anti-inflammatory drug
Function / homology
Function and homology information


hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / positive regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / 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
IBUPROFEN / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsGonzalez, J.M. / Pozharski, E.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structural analysis of ibuprofen binding to human adipocyte fatty-acid binding protein (FABP4).
Authors: Gonzalez, J.M. / Fisher, S.Z.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6922
Polymers15,4861
Non-polymers2061
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.328, 53.380, 75.031
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 Fatty acid-binding protein, adipocyte / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP / Fatty acid-binding protein 4


Mass: 15485.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15090
#2: Chemical ChemComp-IBP / IBUPROFEN / 2-(4-ISOBUTYLPHENYL)PROPIONIC ACID / Dexibuprofen


Mass: 206.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O2 / Comment: antiinflammatory, medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1.6 M sodium citrate, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.06→43.5 Å / Num. all: 58556 / Num. obs: 58556 / % possible obs: 98.4 % / Redundancy: 6.3 % / Rsym value: 0.124 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.06-1.123.80.72510.725194.3
1.12-1.184.30.5381.30.538197.1
1.18-1.276.50.4731.50.473199.5
1.27-1.376.50.3491.90.349199.1
1.37-1.56.50.2592.40.259199.2
1.5-1.686.60.1793.20.179199.8
1.68-1.946.50.1313.90.1311100
1.94-2.378.50.1393.80.1391100
2.37-3.3510.70.1065.20.106199.9
3.35-37.5168.60.087.10.08198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.3.16data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→43.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.636 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflection
Rfree0.191 2355 5.1 %
Rwork0.158 --
obs0.16 46490 99 %
Solvent computationSolvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.03 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---0.13 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.15→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 15 172 1259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221227
X-RAY DIFFRACTIONr_bond_other_d0.0140.02854
X-RAY DIFFRACTIONr_angle_refined_deg2.011.9721663
X-RAY DIFFRACTIONr_angle_other_deg1.0213.0012098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3165166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38424.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5215247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.104157
X-RAY DIFFRACTIONr_chiral_restr0.1120.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021394
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02239
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_it2.1971.5761
X-RAY DIFFRACTIONr_mcbond_other0.7341.5317
X-RAY DIFFRACTIONr_mcangle_it3.35521246
X-RAY DIFFRACTIONr_scbond_it4.8243466
X-RAY DIFFRACTIONr_scangle_it6.774.5412
X-RAY DIFFRACTIONr_rigid_bond_restr2.0432081
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.18 Å
RfactorNum. reflection% reflection
Rfree0.259 157 -
Rwork0.241 3144 -
obs--96.63 %

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