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- PDB-5hz5: FABP5 in complex with 6-Chloro-4-phenyl-2-piperidin-1-yl-3-(1H-te... -

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Basic information

Entry
Database: PDB / ID: 5hz5
TitleFABP5 in complex with 6-Chloro-4-phenyl-2-piperidin-1-yl-3-(1H-tetrazol-5-yl)-quinoline
ComponentsFatty acid-binding protein, epidermal
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 / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity ...regulation of prostaglandin biosynthetic process / regulation of retrograde trans-synaptic signaling by endocanabinoid / lipid transport across blood-brain barrier / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of glucose transmembrane transport / regulation of sensory perception of pain / phosphatidylcholine biosynthetic process / retinoic acid binding / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / fatty acid transport / long-chain 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 / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-65X / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsEhler, A. / Rudolph, M.G.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2016
Title: Design and synthesis of selective, dual fatty acid binding protein 4 and 5 inhibitors.
Authors: Kuhne, H. / Obst-Sander, U. / Kuhn, B. / Conte, A. / Ceccarelli, S.M. / Neidhart, W. / Rudolph, M.G. / Ottaviani, G. / Gasser, R. / So, S.S. / Li, S. / Zhang, X. / Gao, L. / Myers, M.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,6194
Polymers15,0541
Non-polymers5653
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-13 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.790, 62.790, 75.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 15054.262 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, RESIDUES 2-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01469
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-65X / 6-chloro-4-phenyl-2-(piperidin-1-yl)-3-(1H-tetrazol-5-yl)quinoline


Mass: 390.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19ClN6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop

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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: Feb 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.24 Å / Num. obs: 29968 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 22.359 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Net I/σ(I): 15.12
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.4413.82.2140.84197.4
1.44-1.481.3641.58197.7
1.48-1.521.8631.35198.3
1.52-1.571.0672.43198.2
1.57-1.620.7973.08198.8
1.62-1.670.6124.55198.5
1.67-1.740.456.71199.2
1.74-1.810.3379.14199
1.81-1.890.25811.98199.1
1.89-1.980.20714.91197.6
1.98-2.090.14418.84199.6
2.09-2.210.10923.35199.6
2.21-2.370.10525.65198.7
2.37-2.560.0830.241100
2.56-2.80.06833.08199.8
2.8-3.130.05737.321100
3.13-3.620.05243.981100
3.62-4.430.0545.92199.8
4.43-6.260.04845.98199.7
6.260.04747.591100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIX1.10_2155refinement
XDSdata reduction
REFMACphasing
RefinementResolution: 1.4→44.399 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.94
RfactorNum. reflection% reflection
Rfree0.2277 1508 5.04 %
Rwork0.2079 --
obs0.2089 29905 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.93 Å2 / Biso mean: 21.0931 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: final / Resolution: 1.4→44.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1047 0 65 104 1216
Biso mean--23.91 28.12 -
Num. residues----134
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0494-0.06660.01930.25670.04270.1182-0.0336-0.18880.2920.35680.0392-0.4922-0.1492-0.09390.00590.17660.0103-0.00620.1522-0.01360.2025-14.621916.93320.5589
20.0882-0.1261-0.11540.13010.09430.069-0.02320.13380.226-0.21880.0896-0.32730.0073-0.17490.00880.1779-0.02170.06360.14380.0240.1816-9.7433-0.1831-10.8713
30.08460.04650.07220.2271-0.08420.1448-0.00390.24810.1328-0.07-0.0392-0.0621-0.0021-0.0344-0.00160.104-0.00230.02820.1430.00290.1569-18.731116.8016-8.8834
40.14330.03470.02410.1059-0.05250.0419-0.095-0.15860.00480.05970.04630.0060.1097-0.0013-0.00740.1210.0056-0.00050.14750.01010.094-27.47417.8627-8.955
50.3775-0.38390.15510.2998-0.15360.1323-0.0464-0.1570.03350.07390.0045-0.0931-0.0253-0.074-0.0020.11380-0.01010.1073-0.00780.0956-17.84897.8022-0.2973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )A2 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 38 )A18 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 68 )A39 - 68
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 90 )A69 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 135 )A91 - 135

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