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- PDB-5edc: human FABP4 in complex with 6-Chloro-4-phenyl-2-piperidin-1-yl-qu... -

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Basic information

Entry
Database: PDB / ID: 5edc
Titlehuman FABP4 in complex with 6-Chloro-4-phenyl-2-piperidin-1-yl-quinoline-3-carboxylic acid at 1.29A
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 / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / 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 / fatty acid transport / long-chain 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 / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5M7 / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.29 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 25, 2016Group: Database references
Revision 1.2May 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)15,4665
Polymers14,8111
Non-polymers6554
Water2,252125
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-35 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.414, 53.600, 74.488
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: 14810.978 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15090
#2: Chemical ChemComp-5M7 / 6-chloranyl-4-phenyl-2-piperidin-1-yl-quinoline-3-carboxylic acid


Mass: 366.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19ClN2O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES/NaOH pH 7.5, 2.0-2.2 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: Nov 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→43.51 Å / Num. obs: 37129 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.08 % / Biso Wilson estimate: 22.666 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 1.037 / Net I/σ(I): 12.86 / Num. measured all: 228777
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
1.24-1.271.5070.859995274023160.4081.70484.5
1.27-1.311.4541.1816510267626580.5421.58999.3
1.31-1.351.2071.4215961258125650.6911.31999.4
1.35-1.390.9891.7314900253725250.7321.08699.5
1.39-1.430.7472.3915680245624490.8270.81399.7
1.43-1.480.5373.3315324237623670.9180.58499.6
1.48-1.540.4034.4414803230322980.9430.43999.8
1.54-1.60.2646.2813466219821900.9760.28899.6
1.6-1.670.2068.0313523212621250.9820.225100
1.67-1.750.14611.213467202720270.9910.159100
1.75-1.850.10914.4812797194919480.9950.11899.9
1.85-1.960.07719.5911746184918460.9970.08499.8
1.96-2.10.06323.7510368172417210.9970.06999.8
2.1-2.260.05429.1810821163716370.9980.058100
2.26-2.480.04831.579700150715050.9980.05399.9
2.48-2.770.04533.568205136213610.9980.04999.9
2.77-3.20.0436.97237122012160.9980.04499.7
3.2-3.920.03441.376648104810420.9990.03799.4
3.92-5.550.0339.8347168328280.9990.03399.5
5.550.03139.3229105095050.9990.03499.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
REFMACrefinement
XDSdata reduction
REFMACphasing
RefinementResolution: 1.29→43.51 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.399 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 1648 5.2 %RANDOM
Rwork0.1556 ---
obs0.1573 30192 95.18 %-
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: 76.05 Å2 / Biso mean: 19.711 Å2 / Biso min: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2---0.59 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.29→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 67 126 1228
Biso mean--34.32 31.55 -
Num. residues----133
LS refinement shellResolution: 1.29→1.323 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 94 -
Rwork0.313 2006 -
all-2100 -
obs--87.17 %

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