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- PDB-2qm9: Troglitazone Bound to Fatty Acid Binding Protein 4 -

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Basic information

Entry
Database: PDB / ID: 2qm9
TitleTroglitazone Bound to Fatty Acid Binding Protein 4
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / beta clamshell
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / cellular response to lithium ion / long-chain fatty acid binding / white fat cell differentiation / fatty acid transport / long-chain fatty acid transport / brown fat cell differentiation / fatty acid metabolic process / cholesterol homeostasis / fatty acid binding / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / nucleoplasm / nucleus / cytoplasm / 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-TDZ / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsGillilan, R.E. / Ayers, S.D. / Noy, N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for Activation of Fatty Acid-binding Protein 4
Authors: Gillilan, R.E. / Ayers, S.D. / Noy, N.
History
DepositionJul 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600 HETEROGEN According to authors, ligand TDZ is stereochemically impure (modeled as 2R-5R). Atoms ... HETEROGEN According to authors, ligand TDZ is stereochemically impure (modeled as 2R-5R). Atoms with missing density are marked with zero occupancy.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,1747
Polymers34,0032
Non-polymers1,1715
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.886, 81.414, 94.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, adipocyte / AFABP / Adipocyte lipid-binding protein / ALBP / A-FABP / P2 adipocyte protein / Myelin P2 protein ...AFABP / Adipocyte lipid-binding protein / ALBP / A-FABP / P2 adipocyte protein / Myelin P2 protein homolog / 3T3-L1 lipid-binding protein / 422 protein / P15


Mass: 17001.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp4, Ap2 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04117
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TDZ / (5R)-5-(4-{[(2R)-6-HYDROXY-2,5,7,8-TETRAMETHYL-3,4-DIHYDRO-2H-CHROMEN-2-YL]METHOXY}BENZYL)-1,3-THIAZOLIDINE-2,4-DIONE / TROGLITAZONE


Mass: 441.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27NO5S / Comment: antiinflammatory*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4.5
Details: 1.6 M ammonium sulfate, 0.1 M sodium acetate, 0.05 M K/Na phosphate, pH 4.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 17515

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→12 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.401 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 863 5 %RANDOM
Rwork0.231 ---
obs0.233 16232 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.481 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.31→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 77 108 2261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222180
X-RAY DIFFRACTIONr_bond_other_d0.0020.021951
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9972941
X-RAY DIFFRACTIONr_angle_other_deg0.78634530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855269
X-RAY DIFFRACTIONr_chiral_restr0.0830.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_nbd_refined0.2250.2535
X-RAY DIFFRACTIONr_nbd_other0.2410.22642
X-RAY DIFFRACTIONr_nbtor_other0.1120.21649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3680.22
X-RAY DIFFRACTIONr_mcbond_it0.4721.51334
X-RAY DIFFRACTIONr_mcangle_it0.90322149
X-RAY DIFFRACTIONr_scbond_it1.3873846
X-RAY DIFFRACTIONr_scangle_it2.3174.5792
LS refinement shellResolution: 2.307→2.427 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.315 110
Rwork0.265 2179
all-2289
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)
128.3543-19.1606-9.750134.57886.645485.21120.83912.58451.93463.6407-1.1981-1.8991-2.22793.19570.35890.4208-0.0238-0.00830.307-0.1360.87339.5571-23.86911.14
26.4158-4.4912-1.78946.95911.0780.68780.0019-0.87650.28680.4520.01210.3037-0.19030.1262-0.01410.18330.01590.00690.286-0.22930.1862-5.1345-8.148423.9733
33.599-0.53150.33982.32480.24772.12170.022-0.37340.25730.04320.02940.0509-0.1144-0.0388-0.05140.1074-0.02730.01940.0903-0.06330.1243-3.7474-13.100713.4653
47.2553-3.3044-0.93779.2548-0.23481.9523-0.0727-1.0313-0.51250.26550.0289-0.06650.24290.16390.04390.1497-0.01060.00930.23660.14670.1025-20.7933-35.869120.2871
54.2308-0.0143-0.79972.25450.0663.14190.0005-0.4054-0.23730.0220.0130.02390.08950.0655-0.01350.0948-0.00580.00990.08720.0570.0914-21.2619-30.251111.6613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-5 - 319 - 27
2X-RAY DIFFRACTION2AA4 - 4028 - 64
3X-RAY DIFFRACTION3AA41 - 13165 - 155
4X-RAY DIFFRACTION4BB0 - 4024 - 64
5X-RAY DIFFRACTION5BB41 - 13165 - 155

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