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- PDB-7fw8: Crystal Structure of human FABP4 binding site mutated to that of ... -

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Basic information

Entry
Database: PDB / ID: 7fw8
TitleCrystal Structure of human FABP4 binding site mutated to that of FABP3 in complex with 6-chloro-2-methyl-4-phenylquinoline-3-carboxylic acid, i.e. SMILES c1(c(c2c(nc1C)ccc(c2)Cl)c1ccccc1)C(=O)O with IC50=0.275 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-5M8 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsEhler, A. / Benz, J. / Obst, 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)15,6285
Polymers15,0601
Non-polymers5684
Water2,594144
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)32.555, 54.149, 74.859
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-5M8 / 6-chloranyl-2-methyl-4-phenyl-quinoline-3-carboxylic acid


Mass: 297.736 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.16→37.43 Å / Num. obs: 46351 / % possible obs: 99.2 % / Redundancy: 6.15 % / Biso Wilson estimate: 17.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.089 / Rsym value: 0.08 / Χ2: 0.825 / Net I/σ(I): 8.74 / Num. measured all: 288017 / Scaling rejects: 508
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
1.16-1.196.1331.8891.1120367339333210.5662.06197.9
1.19-1.226.0331.651.2919570331432440.6331.80397.9
1.22-1.265.8911.4691.5318786325031890.6921.6198.1
1.26-1.36.4161.0382.119814312530880.7921.12898.8
1.3-1.346.350.9352.4419242305130300.8381.01799.3
1.34-1.396.2340.7493.0218340295029420.8790.81799.7
1.39-1.445.9910.6323.5716924284328250.8950.69299.4
1.44-1.56.5830.4634.917959273327280.9520.50299.8
1.5-1.566.5920.3276.5517449265326470.9720.35599.8
1.56-1.646.5260.2368.916478253025250.9810.25799.8
1.64-1.736.2080.17410.9514874240023960.9870.1999.8
1.73-1.836.460.12614.4514736228322810.9930.13799.9
1.83-1.966.4130.10518.1713537215421110.9950.11598
1.96-2.126.5420.0723.2913123201320060.9970.07699.7
2.12-2.325.7950.06425.4310542187718190.9970.0796.9
2.32-2.595.7870.0528.619676168416720.9980.05699.3
2.59-36.4070.04434.059745152515210.9980.04799.7
3-3.676.0120.03737.587725129312850.9990.0499.4
3.67-5.195.4870.03437.225509102110040.9980.03798.3
5.19-37.435.8310.03438.6136216256210.9980.03799.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0111refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.16→37.43 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.16 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ligand similar in the chimera compared to FABP3, but different to FABP4
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 2211 5.1 %RANDOM
Rwork0.1711 ---
obs0.1735 40954 92.53 %-
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: 64.08 Å2 / Biso mean: 14.927 Å2 / Biso min: 8.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2---0.78 Å20 Å2
3----0.79 Å2
Refinement stepCycle: final / Resolution: 1.16→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1050 0 35 144 1229
Biso mean--24.16 27.58 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221142
X-RAY DIFFRACTIONr_bond_other_d0.0010.02771
X-RAY DIFFRACTIONr_angle_refined_deg2.0762.0031549
X-RAY DIFFRACTIONr_angle_other_deg1.39231900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11224.66745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3156
X-RAY DIFFRACTIONr_chiral_restr0.1230.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021238
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02223
X-RAY DIFFRACTIONr_rigid_bond_restr5.51331913
X-RAY DIFFRACTIONr_sphericity_free19.117547
X-RAY DIFFRACTIONr_sphericity_bonded9.15651993
LS refinement shellResolution: 1.16→1.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 138 -
Rwork0.321 2577 -
all-2715 -
obs--83.82 %

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