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- PDB-1tow: Crystal structure of human adipocyte fatty acid binding protein i... -

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Basic information

Entry
Database: PDB / ID: 1tow
TitleCrystal structure of human adipocyte fatty acid binding protein in complex with a carboxylic acid ligand
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 / long-chain fatty acid binding / cellular response to lithium ion / 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 / long-chain fatty acid binding / cellular response to lithium ion / 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 / positive regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / 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 protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
4-(9H-CARBAZOL-9-YL)BUTANOIC ACID / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsLehmann, F. / Haile, S. / Axen, E. / Medina, C. / Uppenberg, J. / Svensson, S. / Lundback, T. / Rondahl, L. / Barf, T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2004
Title: Discovery of inhibitors of human adipocyte fatty acid-binding protein, a potential type 2 diabetes target.
Authors: Lehmann, F. / Haile, S. / Axen, E. / Medina, C. / Uppenberg, J. / Svensson, S. / Lundback, T. / Rondahl, L. / Barf, T.
History
DepositionJun 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)14,8622
Polymers14,6091
Non-polymers2531
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.050, 53.045, 31.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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) / Production host: Escherichia coli (E. coli) / References: UniProt: P15090
#2: Chemical ChemComp-CRZ / 4-(9H-CARBAZOL-9-YL)BUTANOIC ACID / CARBAZOLE BUTANOIC ACID


Mass: 253.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG2000, DMSO, TRIS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 5, 2000
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 8190 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 55.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 7 / Num. unique all: 577 / % possible all: 67.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.656 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25651 368 4.5 %RANDOM
Rwork0.18848 ---
obs0.19151 7757 93.78 %-
all-7757 --
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 mean: 20.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---1.28 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1022 0 19 174 1215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221056
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9661421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49624.65143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77215200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.525156
X-RAY DIFFRACTIONr_chiral_restr0.0750.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02763
X-RAY DIFFRACTIONr_nbd_refined0.1890.2461
X-RAY DIFFRACTIONr_nbtor_refined0.30.2706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.219
X-RAY DIFFRACTIONr_mcbond_it0.7641.5673
X-RAY DIFFRACTIONr_mcangle_it1.19221051
X-RAY DIFFRACTIONr_scbond_it1.6723464
X-RAY DIFFRACTIONr_scangle_it2.794.5370
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 13 -
Rwork0.226 402 -
obs--68.26 %

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