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- PDB-7fx2: Crystal Structure of human FABP4 binding site mutated to that of ... -

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Basic information

Entry
Database: PDB / ID: 7fx2
TitleCrystal Structure of human FABP4 binding site mutated to that of FABP5 in complex with 2-[[6,6-difluoro-3-(4-methyl-1,3-thiazol-2-yl)-5,7-dihydro-4H-1-benzothiophen-2-yl]carbamoyl]cyclohexene-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
Chem-QJQ / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 binding site mutated to that of FABP5 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)15,4512
Polymers15,0121
Non-polymers4391
Water2,072115
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)31.981, 52.826, 72.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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: 15012.244 Da / Num. of mol.: 1 / Mutation: V24L,V33M,A34G,M41C,S54T,F58L,H94Q,S125C
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-QJQ / 2-{[(3M)-6,6-difluoro-3-(4-methyl-1,3-thiazol-2-yl)-4,5,6,7-tetrahydro-1-benzothiophen-2-yl]carbamoyl}cyclohex-1-ene-1-carboxylic acid


Mass: 438.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20F2N2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.47 %
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: 0.70003 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70003 Å / Relative weight: 1
ReflectionResolution: 1.47→36.11 Å / Num. obs: 21535 / % possible obs: 100 % / Redundancy: 6.53 % / Biso Wilson estimate: 22.779 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.113 / Rsym value: 0.094 / Χ2: 0.838 / Net I/σ(I): 10.86 / Num. measured all: 140082 / Scaling rejects: 14
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
1.47-1.516.7321.5051.1810529156515640.4351.6399.9
1.51-1.556.711.1911.4810032149614950.5471.2999.9
1.55-1.596.5660.9481.929764148714870.6251.028100
1.59-1.646.2770.8062.179076144614460.7390.878100
1.64-1.76.4750.6572.729058139913990.8070.714100
1.7-1.766.7980.5343.489293136813670.8550.57799.9
1.76-1.826.6990.4194.378716130013010.9040.455100
1.82-1.96.5970.35.958365126812680.9570.326100
1.9-1.986.2870.2098.027588120712070.9740.228100
1.98-2.086.3760.1819.627460117011700.9810.198100
2.08-2.196.7150.13312.757514111911190.9920.144100
2.19-2.326.6850.11814.316993104610460.9930.128100
2.32-2.486.5170.10116.4565049989980.9930.11100
2.48-2.686.2170.08518.4358009379330.9950.09399.6
2.68-2.946.6220.06923.6157218648640.9970.075100
2.94-3.296.610.05429.8451567817800.9980.05899.9
3.29-3.86.0860.03937.0842547016990.9990.04299.7
3.8-4.656.1570.03341.9537316066060.9990.036100
4.65-6.576.1050.03241.5129614864850.9990.03599.8
6.57-36.115.2760.02841.0115672992970.9990.03199.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0027refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.47→36.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.506 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Density only observed for hydrolyzed form 2-[[6,6-difluoro-3-(4-methyl-1,3-thiazol-2-yl)-5,7-dihydro-4H-1-benzothiophen-2-yl]carbamoyl]cyclohexene-1-carboxylic acid. Two conformations of ...Details: Density only observed for hydrolyzed form 2-[[6,6-difluoro-3-(4-methyl-1,3-thiazol-2-yl)-5,7-dihydro-4H-1-benzothiophen-2-yl]carbamoyl]cyclohexene-1-carboxylic acid. Two conformations of ligand are built differing in ring pucker of cyclohexene ring.
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 1070 5.2 %RANDOM
Rwork0.1624 ---
obs0.166 19647 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.72 Å2 / Biso mean: 19.442 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.47→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 58 115 1185
Biso mean--23.97 29.62 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021117
X-RAY DIFFRACTIONr_angle_refined_deg1.8492.031520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70624.77344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85515210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.776157
X-RAY DIFFRACTIONr_chiral_restr0.1110.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02824
X-RAY DIFFRACTIONr_rigid_bond_restr3.96431114
X-RAY DIFFRACTIONr_sphericity_free27.992539
X-RAY DIFFRACTIONr_sphericity_bonded14.00951171
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 70 -
Rwork0.295 1350 -
all-1420 -
obs--90.85 %

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