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- PDB-7fyd: Crystal Structure of human FABP5 in complex with 6-chloro-4-pheny... -

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Basic information

Entry
Database: PDB / ID: 7fyd
TitleCrystal Structure of human FABP5 in complex with 6-chloro-4-phenyl-2-propan-2-ylquinoline-3-carboxylic acid, i.e. SMILES c1(ccc2c(c1)c(c1ccccc1)c(c(n2)C(C)C)C(=O)O)Cl with IC50=2.6 microM
ComponentsFatty acid-binding protein 5
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING
Function / homology
Function and homology information


regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / retrograde trans-synaptic signaling by endocannabinoid / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of D-glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / long-chain fatty acid transmembrane transporter activity / Signaling by Retinoic Acid / Triglyceride catabolism / postsynaptic cytosol / epidermis development / postsynaptic density, intracellular component / long-chain fatty acid transport / fatty acid transport / secretory granule membrane / fatty acid binding / lipid metabolic process / glucose metabolic process / azurophil granule lumen / glucose homeostasis / positive regulation of cold-induced thermogenesis / postsynaptic density / lipid binding / synapse / Neutrophil degranulation / glutamatergic synapse / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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
Chem-VLQ / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsEhler, A. / Benz, J. / Obst, U. / Ceccarelli-Simona, M. / 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 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 20, 2024Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0645
Polymers15,4681
Non-polymers5964
Water1,67593
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)61.876, 61.876, 74.547
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

21A-383-

HOH

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Components

#1: Protein Fatty acid-binding protein 5 / Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / ...Epidermal-type fatty acid-binding protein / E-FABP / Fatty acid-binding protein / epidermal / Psoriasis-associated fatty acid-binding protein homolog / PA-FABP


Mass: 15467.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Plasmid: PET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01469
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-VLQ / 6-chloro-4-phenyl-2-(propan-2-yl)quinoline-3-carboxylic acid


Mass: 325.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.67 %
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: Jan 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→47.61 Å / Num. obs: 26023 / % possible obs: 98.6 % / Redundancy: 12.569 % / Biso Wilson estimate: 26.949 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.069 / Χ2: 0.866 / Net I/σ(I): 20.41 / Num. measured all: 327093 / Scaling rejects: 4449
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
1.45-1.4911.7772.3251.1822117191918780.7382.43197.9
1.49-1.5312.341.3522.2821657185817550.7971.41194.5
1.53-1.5713.0691.0782.7123590181818050.8641.12299.3
1.57-1.6213.3820.6134.2423660176817680.9280.637100
1.62-1.6713.1940.5115.0422483170417040.9580.532100
1.67-1.7312.4080.4096.5520498165316520.9680.42699.9
1.73-1.813.3680.289.1421509160916090.9860.291100
1.8-1.8713.8270.20412.521446155315510.9920.21299.9
1.87-1.9611.720.19116.7415752146413440.990.291.8
1.96-2.0513.4480.11521.8619136142914230.9970.11999.6
2.05-2.1611.7210.10324.9415941136813600.9970.10899.4
2.16-2.2910.8650.0928.3713473129112400.9960.09596
2.29-2.4513.5140.06536.0816365121512110.9980.06799.7
2.45-2.6512.9390.0639.8114673113811340.9990.06299.6
2.65-2.912.4760.05244.3913200105810580.9990.054100
2.9-3.2411.4240.04248.89111049739720.9990.04399.9
3.24-3.7412.1750.03958.34104228618560.9990.0499.4
3.74-4.5912.2960.03261.53897673373010.03499.6
4.59-6.4811.1930.02959.2267386026020.9990.031100
6.48-47.6111.7330.02560.74435337337110.02699.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0093refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.45→47.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.687 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: clear ligand density, single close contact of isopropyl with cysteine note: ligand affinities in vitro may change depending on the degree of SS-bond formation
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1107 5.1 %RANDOM
Rwork0.2009 ---
obs0.202 20651 82.65 %-
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: 73.39 Å2 / Biso mean: 19.936 Å2 / Biso min: 10.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.45→47.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 37 93 1167
Biso mean--28.38 30.95 -
Num. residues----133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221143
X-RAY DIFFRACTIONr_bond_other_d0.0010.02769
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.9941553
X-RAY DIFFRACTIONr_angle_other_deg0.9463.0021897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2345150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74725.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.618156
X-RAY DIFFRACTIONr_chiral_restr0.1090.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021260
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02217
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 56 -
Rwork0.482 1231 -
all-1287 -
obs--71.3 %

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