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- PDB-5hz9: human FABP3 in complex with 6-Chloro-2-methyl-4-phenyl-quinoline-... -

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Basic information

Entry
Database: PDB / ID: 5hz9
Titlehuman FABP3 in complex with 6-Chloro-2-methyl-4-phenyl-quinoline-3-carboxylic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FATTY ACID BINDING PROTEIN / CYTOPLASM / LIPID-BINDING / TRANSPORT / PROTEIN BINDING / _PHENIX
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 / 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-5M8 / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.0Dec 14, 2016Provider: 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
B: Fatty acid-binding protein, heart
C: Fatty acid-binding protein, heart
D: Fatty acid-binding protein, heart
E: Fatty acid-binding protein, heart
F: Fatty acid-binding protein, heart
G: Fatty acid-binding protein, heart
H: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,79246
Polymers120,8348
Non-polymers6,95838
Water6,323351
1
A: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2867
Polymers15,1041
Non-polymers1,1816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9886
Polymers15,1041
Non-polymers8845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8925
Polymers15,1041
Non-polymers7884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5944
Polymers15,1041
Non-polymers4903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9886
Polymers15,1041
Non-polymers8845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6905
Polymers15,1041
Non-polymers5864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5238
Polymers15,1041
Non-polymers1,4197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Fatty acid-binding protein, heart
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8315
Polymers15,1041
Non-polymers7274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)186.827, 186.827, 114.204
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, 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 / fabp3


Mass: 15104.246 Da / Num. of mol.: 8 / Fragment: SOLUBLE FORM, RESIDUES 3-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05413
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-5M8 / 6-chloranyl-2-methyl-4-phenyl-quinoline-3-carboxylic acid


Mass: 297.736 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C17H12ClNO2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 4.13 Å3/Da / Density % sol: 70.19 %
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: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.18→48.7 Å / Num. obs: 89756 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 56.289 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Net I/σ(I): 14.43
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.18-2.243.6120.66199.8
2.24-2.313.72.9850.81199.8
2.3-2.362.5050.98199.9
2.36-2.441.8051.41199.9
2.44-2.521.32.021100
2.52-2.611.0152.61199.9
2.61-2.70.7673.481100
2.7-2.810.5564.741100
2.81-2.940.4166.31199.9
2.94-3.080.2889.291100
3.08-3.250.18314.481100
3.25-3.450.12221.161100
3.45-3.680.08926.951100
3.68-3.980.07431.851100
3.98-4.360.05740.481100
4.36-4.870.04251.01199.9
4.87-5.630.04545.09199.9
5.63-6.890.04445.47199.9
6.89-9.750.03354.5199.7
9.750.02461.29197.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
PHENIXrefinement
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house model

Resolution: 2.3→47.187 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2389 4161 5 %
Rwork0.1974 --
obs0.1995 83146 92.65 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 50.781 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 166.55 Å2 / Biso mean: 53.9092 Å2 / Biso min: 25.27 Å2
Baniso -1Baniso -2Baniso -3
1--4.9608 Å2-0 Å20 Å2
2---4.9608 Å20 Å2
3---9.9216 Å2
Refinement stepCycle: final / Resolution: 2.3→47.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8466 0 454 351 9271
Biso mean--76.27 47.5 -
Num. residues----1079
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)
11.12720.09060.49831.36330.50191.5399-0.19770.11320.0294-0.23920.1697-0.1464-0.44440.09990.03260.4517-0.0697-0.01290.2910.0370.2487-18.194747.1007-42.3008
20.98220.5391-0.24321.0717-0.3762.1193-0.23320.1248-0.1194-0.27560.220.07910.40430.02810.03190.4568-0.05190.04210.3137-0.04190.29716.169745.0222-42.0374
30.9687-0.67580.48820.9225-0.00991.4939-0.1802-0.15060.12890.03810.1682-0.0946-0.1009-0.00470.01420.32880.023-0.04270.322-0.04160.310414.732645.44611.8863
41.4862-0.2734-0.39930.5630.36651.7648-0.1621-0.1292-0.03610.02850.16080.08860.06840.07930.02340.31420.00910.01320.26970.05040.2844-16.650449.280212.0453
51.3420.8820.18520.8725-0.54321.48160.0614-0.02890.02-0.027-0.031-0.0202-0.14210.0211-0.02610.37-0.00860.03770.27150.01480.368914.568764.0571-12.9333
61.6156-0.5542-0.72671.1395-0.63241.42240.00820.05670.08820.00790.0186-0.04090.12110.0373-0.02260.36450.0352-0.01240.262-0.00330.275415.378626.3139-16.9817
71.34190.6676-0.42840.85660.56181.6916-0.01110.0224-0.03720.00940.00350.08280.2148-0.0263-0.00180.30190.0035-0.04440.1759-0.00140.2423-17.174929.7886-12.0123
81.6211-0.74320.79531.79290.73881.57830.0405-0.0771-0.01580.01740.0532-0.0085-0.16050.0236-0.07280.32430.01090.02090.2310.00270.2142-18.123466.7322-18.0795
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-1 - 133
2X-RAY DIFFRACTION2chain BB-1 - 133
3X-RAY DIFFRACTION3chain CC-1 - 133
4X-RAY DIFFRACTION4chain DD-1 - 133
5X-RAY DIFFRACTION5chain EE-1 - 133
6X-RAY DIFFRACTION6chain FF0 - 133
7X-RAY DIFFRACTION7chain GG-1 - 133
8X-RAY DIFFRACTION8chain HH-1 - 133

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