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- PDB-7g1k: Crystal Structure of human FABP4 in complex with 4-(4-fluoropheny... -

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Basic information

Entry
Database: PDB / ID: 7g1k
TitleCrystal Structure of human FABP4 in complex with 4-(4-fluorophenyl)sulfanyl-6-methyl-2-phenylpyrimidine-5-carboxylic acid
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
FORMIC ACID / Chem-WOI / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Labadie, S. / 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)15,6796
Polymers15,0221
Non-polymers6575
Water3,063170
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)32.391, 53.685, 75.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-WOI / 4-[(4-fluorophenyl)sulfanyl]-6-methyl-2-phenylpyrimidine-5-carboxylic acid


Mass: 340.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13FN2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.35 %
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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→37.51 Å / Num. obs: 50489 / % possible obs: 99.1 % / Redundancy: 6.04 % / Biso Wilson estimate: 15.079 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rrim(I) all: 0.031 / Rsym value: 0.032 / Χ2: 0.946 / Net I/σ(I): 22.04 / Num. measured all: 304985
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
1.12-1.154.4860.2934.9914827370733050.9470.32989.2
1.15-1.185.90.2566.7421181359435900.9710.28199.9
1.18-1.225.8180.2167.7820481352935200.980.23899.7
1.22-1.255.7860.185919881344434360.9840.20499.8
1.25-1.36.2940.15710.7920883332533180.990.17199.8
1.3-1.346.30.13112.7820256321532150.9920.142100
1.34-1.396.1670.11214.7919006308730820.9930.12399.8
1.39-1.456.0910.09217.6118115298529740.9950.10199.6
1.45-1.516.5530.07422.1618879288128810.9970.08100
1.51-1.596.4910.05827.817884275927550.9980.06399.9
1.59-1.676.3020.04932.7916567263026290.9980.054100
1.67-1.775.890.04137.3314614248824810.9990.04599.7
1.77-1.96.5690.03248.1215588237323730.9990.035100
1.9-2.056.4260.02756.7314104219721950.9990.02999.9
2.05-2.246.1960.02461.712498201720170.9990.027100
2.24-2.515.5930.02261.4410353185918510.9990.02599.6
2.51-2.96.4730.02171.3106231641164110.023100
2.9-3.556.2770.01975.488631415141210.02199.8
3.55-5.025.6130.01675.7861911111110310.01899.3
5.02-37.56.2090.01677.56419168067510.01799.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0119refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.12→37.5 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.872 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: second conformation of Fluoro-phenylsulfanyl group
RfactorNum. reflection% reflectionSelection details
Rfree0.1623 2514 5 %RANDOM
Rwork0.135 ---
obs0.1364 47284 97.9 %-
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: 53.59 Å2 / Biso mean: 13 Å2 / Biso min: 7.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.42 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.12→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 65 175 1280
Biso mean--19.33 24.4 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021228
X-RAY DIFFRACTIONr_bond_other_d0.0080.02819
X-RAY DIFFRACTIONr_angle_refined_deg2.1432.0111670
X-RAY DIFFRACTIONr_angle_other_deg1.52432021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6055161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85125.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98315236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.523156
X-RAY DIFFRACTIONr_chiral_restr0.1350.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021367
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02247
X-RAY DIFFRACTIONr_rigid_bond_restr5.68432047
X-RAY DIFFRACTIONr_sphericity_free19.406543
X-RAY DIFFRACTIONr_sphericity_bonded9.86252159
LS refinement shellResolution: 1.122→1.151 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 143 -
Rwork0.158 2831 -
all-2974 -
obs--84.25 %

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