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- PDB-2nnq: Crystal structure of human adipocyte fatty acid binding protein i... -

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Basic information

Entry
Database: PDB / ID: 2nnq
TitleCrystal structure of human adipocyte fatty acid binding protein in complex with ((2'-(5-ethyl-3,4-diphenyl-1H-pyrazol-1-yl)-3-biphenylyl)oxy)acetic acid
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID TRANSPORT / TRANSPORT / LIPID-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 / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-T4B / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 1.8 Å
AuthorsJacobson, B.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Potent and selective biphenyl azole inhibitors of adipocyte fatty acid binding protein (aFABP).
Authors: Sulsky, R. / Magnin, D.R. / Huang, Y. / Simpkins, L. / Taunk, P. / Patel, M. / Zhu, Y. / Stouch, T.R. / Bassolino-Klimas, D. / Parker, R. / Harrity, T. / Stoffel, R. / Taylor, D.S. / Lavoie, ...Authors: Sulsky, R. / Magnin, D.R. / Huang, Y. / Simpkins, L. / Taunk, P. / Patel, M. / Zhu, Y. / Stouch, T.R. / Bassolino-Klimas, D. / Parker, R. / Harrity, T. / Stoffel, R. / Taylor, D.S. / Lavoie, T.B. / Kish, K. / Jacobson, B.L. / Sheriff, S. / Adam, L.P. / Ewing, W.R. / Robl, J.A.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2012Group: Data collection
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: 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)15,2754
Polymers14,6091
Non-polymers6673
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.620, 53.930, 74.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, adipocyte / AFABP / Adipocyte lipid-binding protein / ALBP / A-FABP


Mass: 14608.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P15090
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-T4B / ((2'-(5-ETHYL-3,4-DIPHENYL-1H-PYRAZOL-1-YL)-3-BIPHENYLYL)OXY)ACETIC ACID


Mass: 474.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H26N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 293 K / pH: 5.6
Details: ~70% saturated ammonium sulfate, pH 5.6, vapor diffusion, hanging drop, temperature 293K, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Apr 22, 1999 / Details: MONOCHROMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→99 Å / Num. obs: 12558 / % possible obs: 78.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.9
Reflection shellResolution: 1.77→1.91 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 3.3 / % possible all: 64.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
X-GENdata reduction
X-GENdata scaling
AMoREphasing
CNX2005refinement
RefinementMethod to determine structure: molecular replacement
Starting model: AP2

Resolution: 1.8→5.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2022639.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1032 10 %RANDOM
Rwork0.188 ---
obs0.193 10359 84.1 %-
all-10359 --
Solvent computationBsol: 73.1434 Å2 / ksol: 0.564375 e/Å3
Displacement parametersBiso mean: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20 Å2
2---1.57 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→5.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 46 152 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.51
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.492
X-RAY DIFFRACTIONc_scbond_it1.752
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.274 95 9.6 %
Rwork0.236 890 -
obs--64.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4T4B.PART4B.TOP

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