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- PDB-7fxh: Crystal Structure of human FABP4 in complex with 2-[(2R)-oxolan-2... -

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Basic information

Entry
Database: PDB / ID: 7fxh
TitleCrystal Structure of human FABP4 in complex with 2-[(2R)-oxolan-2-yl]-4-phenyl-3-(1H-tetrazol-5-yl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine, i.e. SMILES c1(c(c(c2c(n1)CCCCC2)c1ccccc1)C1=NN=NN1)[C@H]1CCCO1 with IC50=0.0496937 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
FORMIC ACID / Chem-RI4 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 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 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)15,91610
Polymers15,0221
Non-polymers8949
Water2,702150
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)32.334, 53.724, 74.805
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, 159 molecules

#2: Chemical ChemComp-RI4 / (3P)-2-[(2R)-oxolan-2-yl]-4-phenyl-3-(1H-tetrazol-5-yl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]pyridine


Mass: 361.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 78.133 Da / Num. of mol.: 2 / 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.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.12 %
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: 0.70049 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70049 Å / Relative weight: 1
ReflectionResolution: 1.02→37.4 Å / Num. obs: 67218 / % possible obs: 100 % / Redundancy: 6.54 % / Biso Wilson estimate: 14.054 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.042 / Rsym value: 0.041 / Χ2: 0.893 / Net I/σ(I): 15.3 / Num. measured all: 434259
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
1.02-1.056.6181.0611.6432602493149260.6811.15299.9
1.05-1.086.5180.7482.2931021476147590.8140.813100
1.08-1.116.3730.5223.2729584464846420.8890.56999.9
1.11-1.145.9760.3884.2426975451845140.9260.42699.9
1.14-1.186.6960.315.6429401439143910.9610.336100
1.18-1.226.7610.2586.7328793426142590.9730.28100
1.22-1.276.7170.2098.2327426408640830.9830.22799.9
1.27-1.326.6620.1719.9626443396939690.9870.185100
1.32-1.386.4850.14112.0124681380638060.9890.153100
1.38-1.446.0440.11614.0521873362136190.9920.12799.9
1.44-1.526.8970.09118.9224050348834870.9960.099100
1.52-1.616.840.06725.1722497329032890.9980.073100
1.61-1.726.7120.05630.0720747309130910.9980.061100
1.72-1.866.4480.04436.9318640289128910.9980.047100
1.86-2.045.7260.03443.5415438269726960.9990.037100
2.04-2.286.3910.0352.0515459241924190.9990.033100
2.28-2.636.3580.02756.7513829217521750.9990.029100
2.63-3.236.0480.02459.7711195185218510.9990.02799.9
3.23-4.565.5770.0262.581761472146610.02299.6
4.56-37.46.2190.01765.41542987987310.01899.3

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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: 1.02→37.4 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.766 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: R-enantiomer clearly based on electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.1598 3297 5.1 %RANDOM
Rwork0.138 ---
obs0.1391 61932 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.1 Å2 / Biso mean: 15.612 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2--0 Å20 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 1.02→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 80 155 1281
Biso mean--16.35 25.69 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021245
X-RAY DIFFRACTIONr_bond_other_d0.0020.021244
X-RAY DIFFRACTIONr_angle_refined_deg2.4941.9991691
X-RAY DIFFRACTIONr_angle_other_deg0.9843.0032852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4224.61552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89515248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.322158
X-RAY DIFFRACTIONr_chiral_restr0.150.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02263
X-RAY DIFFRACTIONr_rigid_bond_restr6.52532489
X-RAY DIFFRACTIONr_sphericity_free24.323551
X-RAY DIFFRACTIONr_sphericity_bonded13.75952559
LS refinement shellResolution: 1.02→1.046 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 213 -
Rwork0.312 4237 -
all-4450 -
obs--90.37 %

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