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- PDB-5d4a: Crystal Structure of FABP4 in complex with 3-(2-phenyl-1H-indol-1... -

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Basic information

Entry
Database: PDB / ID: 5d4a
TitleCrystal Structure of FABP4 in complex with 3-(2-phenyl-1H-indol-1-yl)propanoic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN
Function / homology
Function and homology information


hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / Triglyceride catabolism / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytoplasm / 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
3-(2-phenyl-1H-indol-1-yl)propanoic acid / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. ...Tagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. / Kashiwagi, T. / Ishikawa, K. / Miyano, H. / Mizukoshi, T.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis
Authors: Tagami, U. / Takahashi, K. / Igarashi, S. / Ejima, C. / Yoshida, T. / Takeshita, S. / Miyanaga, W. / Sugiki, M. / Tokumasu, M. / Hatanaka, T. / Kashiwagi, T. / Ishikawa, K. / Miyano, H. / Mizukoshi, T.
History
DepositionAug 7, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1772
Polymers16,9111
Non-polymers2651
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7310 Å2
Unit cell
Length a, b, c (Å)32.161, 53.719, 74.291
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 / AFABP / Fatty ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty acid-binding protein 4


Mass: 16911.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P15090
#2: Chemical ChemComp-57Q / 3-(2-phenyl-1H-indol-1-yl)propanoic acid


Mass: 265.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 2.4 M NaH2PO4/K2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 16778 / % possible obs: 95.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.064 / Χ2: 1.846 / Net I/av σ(I): 39.656 / Net I/σ(I): 15.3 / Num. measured all: 106879
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.6650.32514220.70183.4
1.66-1.725.60.27515230.78487.6
1.72-1.86.20.24515950.94692.5
1.8-1.96.40.19616971.23497.1
1.9-2.026.50.14516811.73296.9
2.02-2.176.60.11816812.10496.9
2.17-2.396.60.09717252.44198.6
2.39-2.746.80.0817682.49699.7
2.74-3.4570.05817962.665100
3.45-506.70.03918902.25798.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALEPACKdata scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HNX

2hnx


Resolution: 1.7→43.53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.113 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.223 716 5 %RANDOM
Rwork0.185 ---
obs0.187 13577 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å20 Å2
2---0.98 Å20 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 20 113 1194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4781.9691474
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45824.22245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89715208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.301157
X-RAY DIFFRACTIONr_chiral_restr0.3810.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02797
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 46 -
Rwork0.234 815 -
obs--89.87 %

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