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- PDB-7fw1: Crystal Structure of human FABP4 in complex with 2-cyclopentyl-4-... -

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Basic information

Entry
Database: PDB / ID: 7fw1
TitleCrystal Structure of human FABP4 in complex with 2-cyclopentyl-4-(4-fluorophenyl)-6-[1-(methoxymethyl)cyclopentyl]-3-methyl-5-(1H-tetrazol-5-yl)pyridine
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 / 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 / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
Chem-K7C / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Kuhne, H. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human FABP4 complex
Authors: Obst, U. / Magnone, C. / Kuhn, B. / Rudolph, M.G.
History
DepositionApr 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)15,6504
Polymers15,0221
Non-polymers6283
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.561, 54.055, 74.793
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 / 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
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) / 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-K7C / (5P)-2-cyclopentyl-4-(4-fluorophenyl)-6-[1-(methoxymethyl)cyclopentyl]-3-methyl-5-(1H-tetrazol-5-yl)pyridine


Mass: 435.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30FN5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.86 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.70001 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70001 Å / Relative weight: 1
ReflectionResolution: 1.26→30.75 Å / Num. obs: 36410 / % possible obs: 99.7 % / Redundancy: 6.282 % / Biso Wilson estimate: 20.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.079 / Χ2: 0.845 / Net I/σ(I): 12.18 / Num. measured all: 228727 / Scaling rejects: 56
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
1.26-1.296.4931.1871.5117147265126410.6271.28999.6
1.29-1.336.4881.0121.7916647257325660.7281.199.7
1.33-1.376.3660.8892.0716145254225360.7610.96899.8
1.37-1.416.3130.762.4615448245224470.7930.82899.8
1.41-1.455.990.553.2814118236023570.8660.60399.9
1.45-1.516.0210.453.9714011233123270.9060.49399.8
1.51-1.566.620.345.6614584220822030.9470.3799.8
1.56-1.636.5340.257.614127216621620.9690.27299.8
1.63-1.76.5190.2069.0713358205420490.980.22599.8
1.7-1.786.3830.15511.5712472195719540.9880.16999.8
1.78-1.885.9360.11414.5311214189618890.9920.12599.6
1.88-1.996.1160.07919.2910924178917860.9960.08799.8
1.99-2.136.510.06723.3910865167616690.9960.07399.6
2.13-2.36.3560.05926.149985157915710.9960.06499.5
2.3-2.526.1610.05427.428946146514520.9970.05999.1
2.52-2.825.7010.04828.577491132113140.9960.05399.5
2.82-3.256.3440.04532.247549119611900.9960.04999.5
3.25-3.986.3110.04735.26349100910060.9950.05199.7
3.98-5.635.610.05233.7445228098060.9960.05799.6
5.63-30.755.8250.04433.4228254914850.9980.04898.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.26→30.75 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.222 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Clear density for ligand. Repulsive contacts between cyclopentyl substituent in 6-position and Asp76-Arg78 salt bridge.
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1821 5.2 %RANDOM
Rwork0.1658 ---
obs0.1684 33006 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.24 Å2 / Biso mean: 18.822 Å2 / Biso min: 6.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0 Å2
2--1.15 Å20 Å2
3----0.72 Å2
Refinement stepCycle: final / Resolution: 1.26→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 71 112 1223
Biso mean--20.7 27.7 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021160
X-RAY DIFFRACTIONr_bond_other_d0.0010.021147
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9931581
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0022621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03225.29451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88515221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.318156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_rigid_bond_restr4.26532307
X-RAY DIFFRACTIONr_sphericity_free25.272536
X-RAY DIFFRACTIONr_sphericity_bonded11.16252357
LS refinement shellResolution: 1.26→1.293 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 112 -
Rwork0.292 2271 -
all-2383 -
obs--89.99 %

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