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- PDB-4azm: Human epidermal fatty acid-binding protein (FABP5) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4azm
TitleHuman epidermal fatty acid-binding protein (FABP5) in complex with the inhibitor BMS-309413
ComponentsFATTY ACID-BINDING PROTEIN, EPIDERMAL
KeywordsLIPID BINDING PROTEIN / LIPID CARRIER PROTEIN / ENDOCANNABINOID / BETA-BARREL / BETA-CLAMSHELL / DOMAIN SWAPPING
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 / Signaling by Retinoic Acid / long-chain fatty acid transmembrane transporter activity / Triglyceride catabolism / epidermis development / postsynaptic cytosol / long-chain fatty acid transport / fatty acid transport / postsynaptic density, intracellular component / 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 / synapse / lipid binding / Neutrophil degranulation / glutamatergic synapse / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / 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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-T4B / Fatty acid-binding protein 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSanson, B. / Wang, T. / Sun, J. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Crystallographic Study of Fabp5 as an Intracellular Endocannabinoid Transporter.
Authors: Sanson, B. / Wang, T. / Sun, J. / Wang, L. / Kaczocha, M. / Ojima, I. / Deutsch, D. / Li, H.
History
DepositionJun 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID-BINDING PROTEIN, EPIDERMAL
B: FATTY ACID-BINDING PROTEIN, EPIDERMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9775
Polymers30,9352
Non-polymers1,0413
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-53.9 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.670, 104.670, 58.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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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: 15467.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EPIDERMIS / Cell: KERATINOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01469
#2: Chemical ChemComp-T4B / ((2'-(5-ETHYL-3,4-DIPHENYL-1H-PYRAZOL-1-YL)-3-BIPHENYLYL)OXY)ACETIC ACID


Mass: 474.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H26N2O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITIONAL 3 N-TERM AMINO ACIDS, GSH, LEFT AFTER REMOVAL OF POLY-HIS TAG

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.32 M SODIUM CITRATE, 0.1 M HEPES PH 7.0, SATURATED WITH RESPECT TO BMS-309403, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K. CRYOPROTECTION: 28% GLYCEROL IN MOTHER LIQUOR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2011
RadiationMonochromator: DOUBLE SILICON(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 8919 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 72.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B56

1b56


Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 28.966 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25195 444 5 %RANDOM
Rwork0.20503 ---
obs0.20739 8446 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.217 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 78 44 2223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222209
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.452.0032966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21725.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27815426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1231512
X-RAY DIFFRACTIONr_chiral_restr0.0920.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021604
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.361.51335
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73922158
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2773874
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1484.5808
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 31 -
Rwork0.258 606 -
obs--100 %
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)
15.062-1.2904-0.84832.02151.95782.102-0.1468-0.2898-0.01980.21260.1412-0.10090.0811-0.0810.00560.17090.07790.00080.1930.04870.097532.443516.0285-8.3235
23.781-1.67550.10377.2776-0.92042.4796-0.1504-0.1894-0.26530.09370.23010.67740.1311-0.4226-0.07980.0308-0.00570.02050.22050.06690.093626.72-2.465524.0154
35.0311-2.25921.35594.0998-0.4363.96940.15560.2811-0.2179-0.26510.00670.2407-0.1965-0.4197-0.16230.15920.0685-0.00230.17730.02940.110727.63924.327319.6284
48.1891-1.1138-0.60942.40950.062.0818-0.10270.06250.29380.03350.0562-0.0602-0.19040.00720.04650.1290.04820.04140.05120.04240.044737.252420.8415-12.0746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 58
2X-RAY DIFFRACTION2A59 - 134
3X-RAY DIFFRACTION3B2 - 59
4X-RAY DIFFRACTION4B60 - 135

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