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- PDB-7fxu: Crystal Structure of human FABP4 in complex with 2-[[3-(3-cyclopr... -

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Basic information

Entry
Database: PDB / ID: 7fxu
TitleCrystal Structure of human FABP4 in complex with 2-[[3-(3-cyclopropyl-1,2,4-oxadiazol-5-yl)-4,5-dimethylthiophen-2-yl]carbamoyl]cyclopentene-1-carboxylic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
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 / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / 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 / long-chain fatty acid transport / brown fat cell differentiation / fatty acid transport / 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 / cytosol / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
FORMIC ACID / Chem-U6O / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Richter, H. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP4 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)15,7126
Polymers15,0221
Non-polymers6905
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.123, 54.986, 74.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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: 15022.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090

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Non-polymers , 5 types, 93 molecules

#2: Chemical ChemComp-U6O / 2-{[(3M)-3-(3-cyclopropyl-1,2,4-oxadiazol-5-yl)-4,5-dimethylthiophen-2-yl]carbamoyl}cyclopent-1-ene-1-carboxylic acid


Mass: 373.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein in 25mM Tris/HCl pH 7.5 100mM NaCl, see also PMID 27658368

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.70001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70001 Å / Relative weight: 1
ReflectionResolution: 1.96→37.01 Å / Num. obs: 10815 / % possible obs: 99.9 % / Redundancy: 6.21 % / Biso Wilson estimate: 34.272 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.193 / Rrim(I) all: 0.201 / Rsym value: 0.193 / Χ2: 0.735 / Net I/σ(I): 6.66 / Num. measured all: 66780 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.96-2.016.0451.3731.2446127627630.5111.503100
2.01-2.076.0281.351.2946607757730.5461.47899.7
2.07-2.136.4651.1541.647587367360.5821.256100
2.13-2.196.4260.9861.8947107337330.6931.073100
2.19-2.266.3660.8592.2143166786780.7250.938100
2.26-2.346.1690.7822.5343067006980.7580.85599.7
2.34-2.435.8950.6972.6337736406400.7510.765100
2.43-2.535.9880.6233.0738566456440.8460.68499.8
2.53-2.646.3290.4814.0538866146140.9210.525100
2.64-2.776.3690.3425.4936565745740.9620.373100
2.77-2.926.3750.2916.4236215685680.9690.317100
2.92-3.16.2340.2357.7932485225210.9820.25799.8
3.1-3.316.0180.1511.3130515085070.9890.16499.8
3.31-3.586.3650.09915.3729794684680.9950.108100
3.58-3.926.3820.08217.8628084414400.9970.08999.8
3.92-4.386.2280.06421.5824543953940.9970.0799.7
4.38-5.065.730.05822.4420573593590.9970.064100
5.06-6.26.0630.06421.8518373033030.9960.071100
6.2-8.775.6220.05921.1314002492490.9970.065100
8.77-37.015.0450.04625.297921601570.9980.05198.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0018refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.96→37.01 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.161 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Phe57 disordered
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 514 5 %RANDOM
Rwork0.1898 ---
obs0.1941 9707 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.27 Å2 / Biso mean: 28.037 Å2 / Biso min: 13.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å20 Å2
2---0.5 Å20 Å2
3----1.66 Å2
Refinement stepCycle: final / Resolution: 1.96→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 43 88 1177
Biso mean--36.64 32.14 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191116
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9911506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25224.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31715209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.62156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02811
X-RAY DIFFRACTIONr_rigid_bond_restr3.26731116
X-RAY DIFFRACTIONr_sphericity_free19.301541
X-RAY DIFFRACTIONr_sphericity_bonded10.27851149
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 29 -
Rwork0.267 655 -
all-684 -
obs--90 %

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