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- PDB-8s1k: Crystal Structure of human FABP4 in complex with 2-[1-(methoxymet... -

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Basic information

Entry
Database: PDB / ID: 8s1k
TitleCrystal Structure of human FABP4 in complex with 2-[1-(methoxymethyl)cyclopentyl]-6-pentyl-4-phenyl-3-(1H-tetrazol-5-yl)-5,6,7,8-tetrahydroquinoline
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 / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / 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 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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
: / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsEhler, A. / Benz, J. / Obst-Sander, U. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: A high-resolution data set of fatty acid-binding protein structures. I. Dynamics of FABP4 and ligand binding.
Authors: Casagrande, F. / Ehler, A. / Burger, D. / Benz, J. / Ross, A. / Rudolph, M.G.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: A high-resolution data set of fatty acid-binding protein structures. II. Crystallographic overview, ligand classes and binding pose.
Authors: Ehler, A. / Benz, J. / Rudolph, M.G.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2025
Title: A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.
Authors: Ehler, A. / Bartelmus, C. / Benz, J. / Plitzko, I. / Rudolph, M.G.
History
DepositionFeb 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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)15,5603
Polymers15,0221
Non-polymers5382
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-0 kcal/mol
Surface area7150 Å2
Unit cell
Length a, b, c (Å)31.988, 53.400, 72.131
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: 15022.176 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 3-132
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) / Strain (production host): BL21(DE3) / References: UniProt: P15090
#2: Chemical ChemComp-A1H4Y / (6~{S})-2-[1-(methoxymethyl)cyclopentyl]-6-pentyl-4-phenyl-3-(1~{H}-1,2,3,4-tetrazol-5-yl)-5,6,7,8-tetrahydroquinoline


Mass: 459.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H37N5O / 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.: 154 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.22→42.92 Å / Num. obs: 36560 / % possible obs: 97.1 % / Redundancy: 6.104 % / Biso Wilson estimate: 15.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.093 / Χ2: 0.936 / Net I/σ(I): 9.02 / Num. measured all: 223150
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
1.22-1.256.0841.2251.2114911274624510.5451.33889.3
1.25-1.296.5141.0551.5716323266125060.6411.14794.2
1.29-1.326.360.8042.0415874260424960.7830.87595.9
1.32-1.366.1780.6362.5914913251024140.8280.69596.2
1.36-1.416.6920.4993.5115934246123810.9120.54196.7
1.41-1.466.6120.3984.4515300236623140.9330.43397.8
1.46-1.516.4290.3025.714484230522530.9570.32997.7
1.51-1.586.0070.247.112922220221510.9650.26397.7
1.58-1.656.5440.1988.9513691212120920.9760.21598.6
1.65-1.736.470.16910.512978204320060.9830.18498.2
1.73-1.826.1710.1411.9611787192719100.9870.15399.1
1.82-1.935.6230.11513.6910268185118260.9890.12798.6
1.93-2.065.7060.115.739758173417100.9910.1198.6
2.06-2.235.7490.08817.119279162616140.9920.09799.3
2.23-2.445.4880.08417.438238150715010.9940.09299.6
2.44-2.735.0970.07517.746881136213500.9950.08399.1
2.73-3.155.3770.07319.256549122612180.9950.0899.3
3.15-3.865.5690.06720.775786103910390.9970.073100
3.86-5.465.2860.05820.4743668348260.9960.06399
5.46-42.9195.7930.04421.1629085105020.9980.04898.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1391refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.22→42.919 Å / FOM work R set: 0.8467 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.06 / Stereochemistry target values: ML
Details: S-enantiomer bound. Pentyl chain flexible, last two atoms in particular are not well defined by electron density
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1848 5.06 %RANDOM
Rwork0.1711 34674 --
obs0.1729 36522 97.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.97 Å2 / Biso mean: 19.93 Å2 / Biso min: 10.61 Å2
Refinement stepCycle: final / Resolution: 1.22→42.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1016 0 74 155 1245
Biso mean--18.41 28.05 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091091
X-RAY DIFFRACTIONf_angle_d1.2591476
X-RAY DIFFRACTIONf_chiral_restr0.075169
X-RAY DIFFRACTIONf_plane_restr0.006183
X-RAY DIFFRACTIONf_dihedral_angle_d12.496433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.22-1.2530.31891220.2682242289
1.253-1.28990.29091200.2454255694
1.2899-1.33150.26391540.2354258396
1.3315-1.37910.24291430.203259897
1.3791-1.43430.23851350.1752263597
1.4343-1.49960.21821270.1508266698
1.4996-1.57870.20681440.142267798
1.5787-1.67760.22631330.1436269298
1.6776-1.80710.1841310.1415270799
1.8071-1.9890.17711590.1513270799
1.989-2.27680.18941330.1582276599
2.2768-2.86840.21181860.1812274099
2.8684-42.90.20391610.17922926100

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