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- PDB-5edb: human fatty acid binding protein 4 in complex with 6-Chloro-2-met... -

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Basic information

Entry
Database: PDB / ID: 5edb
Titlehuman fatty acid binding protein 4 in complex with 6-Chloro-2-methyl-4-phenyl-quinoline-3-carboxylic acid at 1.18A
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 / cytoplasm / cytosol
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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5M8 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.18 Å
AuthorsRudolph, M.G. / Ehler, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: A Real-World Perspective on Molecular Design.
Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M.
History
DepositionOct 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,2632
Polymers14,9651
Non-polymers2981
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.297, 54.025, 75.462
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 / AFABP / Fatty ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty acid-binding protein 4


Mass: 14965.123 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 44-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES/NaOH pJ 7.5, 2-2.2 M ammonium sulfate

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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: Jun 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→43.93 Å / Num. obs: 44284 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.13 % / Biso Wilson estimate: 17.249 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.048 / Χ2: 1.024 / Net I/σ(I): 18.31 / Num. measured all: 272461
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.18-1.210.5582.6213184327629320.8390.63189.5
1.21-1.240.4783.8419387318531670.9250.52299.4
1.24-1.270.4154.3318645307830590.9370.45499.4
1.27-1.310.3434.9417619301729830.9540.37698.9
1.31-1.360.2786.318816292629080.9710.30399.4
1.36-1.40.2357.4618285285128460.9760.25699.8
1.4-1.460.1789.5117260272127110.9850.19499.6
1.46-1.520.15310.8415749263126080.9870.16799.1
1.52-1.580.10715.3316782253725280.9940.11799.6
1.58-1.660.08418.8516033243524320.9960.09199.9
1.66-1.750.06922.8715053232023110.9970.07599.6
1.75-1.860.05626.5513250220321880.9970.06199.3
1.86-1.990.04732.8213263205620480.9980.05299.6
1.99-2.150.04237.812686193719310.9980.04599.7
2.15-2.350.0439.9111270179217820.9980.04399.4
2.35-2.630.03640.179257162716150.9990.0499.3
2.63-3.030.03345.089135145314450.9990.03699.4
3.03-3.720.0348.587800124812300.9990.03398.6
3.72-5.260.02746.4754829879730.9990.0398.6
5.260.02747.1235055995870.9980.0398

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementResolution: 1.18→37.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1773 -5 %random
Rwork0.1479 ---
obs-44810 96.4 %-
Displacement parametersBiso max: 59.94 Å2 / Biso mean: 17.3655 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: LAST / Resolution: 1.18→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 21 171 1238

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