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- PDB-7fy9: Crystal Structure of human FABP4 binding site mutated to that of ... -

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Basic information

Entry
Database: PDB / ID: 7fy9
TitleCrystal Structure of human FABP4 binding site mutated to that of FABP5 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: 1.74 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 binding site mutated to that of FABP5 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

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5263
Polymers15,0121
Non-polymers5142
Water1,20767
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)31.672, 53.455, 72.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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: 15012.244 Da / Num. of mol.: 1 / Mutation: V24L,V33M,A34G,M41C,S54T,F58L,H94Q,S125C
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-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
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.04 Å3/Da / Density % sol: 39.75 %
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: 1.00004 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.74→43.01 Å / Num. obs: 12988 / % possible obs: 98.2 % / Redundancy: 6.24 % / Biso Wilson estimate: 20.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.171 / Rrim(I) all: 0.164 / Rsym value: 0.171 / Χ2: 0.779 / Net I/σ(I): 6.1 / Num. measured all: 80744 / Scaling rejects: 1
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
1.74-1.796.5782.2581.2760789559240.4462.45196.8
1.79-1.836.6021.961.5360879459220.5082.12897.6
1.83-1.896.4081.4912.0656018968740.6551.62397.5
1.89-1.956.1041.2882.3851768778480.6631.40996.7
1.95-2.016.2210.9283.351458538270.7921.01397
2.01-2.086.4580.7234.252708408160.8670.78697.1
2.08-2.166.270.5585.2648287907700.9240.60997.5
2.16-2.256.1220.4256.6447267897720.950.46497.8
2.25-2.355.8480.3867.4441997307180.9450.42498.4
2.35-2.466.1290.3139.2243647237120.9760.34198.5
2.46-2.596.4870.27410.5343986866780.9840.29898.8
2.59-2.756.5960.22312.7941626396310.9860.24298.7
2.75-2.946.3520.16314.9338246086020.9920.17899
2.94-3.186.0420.11718.0834865875770.9930.12898.3
3.18-3.486.5140.07824.8533745235180.9970.08499
3.48-3.896.2510.06227.2229944854790.9980.06898.8
3.89-4.495.4590.05528.5223424344290.9980.06198.8
4.49-5.55.7750.04732.0221603773740.9970.05299.2
5.5-7.785.4290.04728.6916343023010.9980.05299.7
7.78-43.0064.7910.03430.968961901870.9980.03798.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.74→43.006 Å / FOM work R set: 0.7753 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 692 5.34 %RANDOM
Rwork0.2047 12268 --
obs0.2083 12960 98.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.95 Å2 / Biso mean: 18.37 Å2 / Biso min: 4.24 Å2
Refinement stepCycle: final / Resolution: 1.74→43.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 65 67 1144
Biso mean--22.79 22.75 -
Num. residues----130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131076
X-RAY DIFFRACTIONf_angle_d1.4551452
X-RAY DIFFRACTIONf_chiral_restr0.078167
X-RAY DIFFRACTIONf_plane_restr0.006179
X-RAY DIFFRACTIONf_dihedral_angle_d16.801403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.87440.35151310.27742381251297
1.8744-2.0630.36691210.24182374249597
2.063-2.36150.25561310.21042424255598
2.3615-2.97520.29231650.20192472263799
2.9752-43.01870.23611440.184626172761100

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