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- PDB-8zci: X-ray structure of the human heart fatty acid-binding protein com... -

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Basic information

Entry
Database: PDB / ID: 8zci
TitleX-ray structure of the human heart fatty acid-binding protein complexed with R-Ibuprofen
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP / Complex / Binding protein / R-Ibuprofen
Function / homology
Function and homology information


positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport ...positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / oleic acid binding / phospholipid homeostasis / long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
ACETIC ACID / (2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSugiyama, S. / Tanaka, J. / Matsuoka, S. / Murata, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER1005 Japan
Japan Science and TechnologyJPMJTM19DC Japan
Other private09-003-005 Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
CitationJournal: To Be Published
Title: X-ray structure of the human heart fatty acid-binding protein complexed with R-Ibuprofen
Authors: Sugiyama, S. / Tanaka, J. / Matsuoka, S. / Murata, M.
History
DepositionApr 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,6887
Polymers14,8791
Non-polymers8096
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint14 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.201, 107.868, 48.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fatty acid-binding protein, heart / Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived ...Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived growth inhibitor / MDGI / Muscle fatty acid-binding protein / M-FABP


Mass: 14879.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413

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Non-polymers , 7 types, 200 molecules

#2: Chemical ChemComp-IZP / (2R)-2-[4-(2-methylpropyl)phenyl]propanoic acid / (R)-Ibuprofen


Mass: 206.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M Na-citrate (pH4.5), 40%PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.35→58.24 Å / Num. obs: 39678 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.4
Reflection shellResolution: 1.35→1.37 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1968

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WVM

3wvm


Resolution: 1.35→31.93 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.923 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16569 1987 5 %RANDOM
Rwork0.13238 ---
obs0.13409 37593 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.079 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å2-0 Å2
2---0.04 Å20 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 1.35→31.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 55 194 1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131213
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171182
X-RAY DIFFRACTIONr_angle_refined_deg1.691.6621641
X-RAY DIFFRACTIONr_angle_other_deg1.4311.6062756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6435155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49424.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27115223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.421154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021346
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02234
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7721.929591
X-RAY DIFFRACTIONr_mcbond_other2.5761.922589
X-RAY DIFFRACTIONr_mcangle_it3.2122.896755
X-RAY DIFFRACTIONr_mcangle_other3.2622.902756
X-RAY DIFFRACTIONr_scbond_it3.9572.425622
X-RAY DIFFRACTIONr_scbond_other3.9552.431623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6383.446887
X-RAY DIFFRACTIONr_long_range_B_refined5.8826.3221303
X-RAY DIFFRACTIONr_long_range_B_other5.4124.9841249
X-RAY DIFFRACTIONr_rigid_bond_restr2.74932394
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 133 -
Rwork0.267 2716 -
obs--97.84 %

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