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- PDB-7fwm: Crystal Structure of human FABP4 binding site mutated to that of ... -

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Basic information

Entry
Database: PDB / ID: 7fwm
TitleCrystal Structure of human FABP4 binding site mutated to that of FABP3 in complex with 1-[(4-chloro-2-phenylphenyl)methyl]-4-hydroxypyridin-2-one, i.e. SMILES C1(=CC(=O)N(C=C1)Cc1ccc(cc1c1ccccc1)Cl)O with IC50=2.3 microM
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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
Chem-O9U / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Obst-Sander, U. / 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 binding site mutated to that of FABP3 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / struct
Item: _pdbx_entry_details.has_protein_modification / _struct.title

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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)15,4523
Polymers15,0601
Non-polymers3922
Water4,179232
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)35.456, 55.698, 74.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 15060.242 Da / Num. of mol.: 1 / Mutation: V23L,M40T,I51L,S53T,I104L,V115L,C117L,S124C
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
#2: Chemical ChemComp-O9U / 1-[(5-chloro[1,1'-biphenyl]-2-yl)methyl]-4-hydroxy-5,6-dihydropyridin-2(1H)-one


Mass: 313.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 49.9 %
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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.17→37.44 Å / Num. obs: 49500 / % possible obs: 98.1 % / Redundancy: 5.25 % / Biso Wilson estimate: 16.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.047 / Rsym value: 0.044 / Χ2: 0.915 / Net I/σ(I): 14.04 / Num. measured all: 262778 / Scaling rejects: 499
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
1.17-1.22.6730.4232.137912367929600.8430.51280.5
1.2-1.243.7470.3923.0213236357435320.8980.45498.8
1.24-1.274.140.3733.3914359351234680.9230.42798.7
1.27-1.314.3480.3423.9914367337633040.9290.38997.9
1.31-1.365.1740.2755.2416991329232840.9670.30699.8
1.36-1.45.5420.2416.1617667319331880.9720.26799.8
1.4-1.465.7330.1957.8917481306130490.9840.21599.6
1.46-1.515.5010.1659.6316295297629620.9850.18299.5
1.51-1.586.2640.11913.3917877286228540.9930.1399.7
1.58-1.666.3590.09516.2517162271426990.9950.10399.4
1.66-1.756.2830.07720.1616337261726000.9960.08499.4
1.75-1.865.7770.06422.7614032246524290.9970.07198.5
1.86-1.986.0980.05429.7714117233023150.9980.05999.4
1.98-2.146.360.04434.8913775217721660.9990.04899.5
2.14-2.355.9610.04237.5311892201419950.9980.04799.1
2.35-2.625.580.03838.4110028181617970.9980.04299
2.62-3.036.2730.03244.3110213163416280.9990.03599.6
3.03-3.716.2650.02947.968689139913870.9990.03199.1
3.71-5.255.6280.02546.566196110811010.9990.02799.4
5.25-37.446.2440.02148.741526706650.9990.02399.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0093refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.17→37.44 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.546 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 2360 5 %RANDOM
Rwork0.1586 ---
obs0.1604 45024 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 47.43 Å2 / Biso mean: 13.393 Å2 / Biso min: 7.85 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2---0.67 Å20 Å2
3----0.97 Å2
Refinement stepCycle: final / Resolution: 1.17→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 26 234 1314
Biso mean--16.2 25.99 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221143
X-RAY DIFFRACTIONr_bond_other_d0.0020.02782
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9871547
X-RAY DIFFRACTIONr_angle_other_deg1.05531924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.845148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95724.56546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59815224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.593156
X-RAY DIFFRACTIONr_chiral_restr0.120.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021257
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02229
X-RAY DIFFRACTIONr_rigid_bond_restr4.38936442
X-RAY DIFFRACTIONr_sphericity_free13.8645235
X-RAY DIFFRACTIONr_sphericity_bonded5.63351902
LS refinement shellResolution: 1.173→1.204 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 103 -
Rwork0.262 2357 -
all-2460 -
obs--69.75 %

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