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- PDB-3qj9: Crystal structure of fatty acid amide hydrolase with small molecu... -

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Basic information

Entry
Database: PDB / ID: 3qj9
TitleCrystal structure of fatty acid amide hydrolase with small molecule inhibitor
ComponentsFatty-acid amide hydrolase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protein-inhibitor complex / FAAH / Fatty-acid amide hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Arachidonic acid metabolism / fatty acid amide hydrolase / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / acylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / organelle membrane ...Arachidonic acid metabolism / fatty acid amide hydrolase / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / acylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / organelle membrane / positive regulation of vasoconstriction / fatty acid metabolic process / phospholipid binding / Golgi membrane / lipid binding / endoplasmic reticulum membrane / identical protein binding
Similarity search - Function
Amidase, conserved site / Amidases signature. / Amidase signature (AS) enzymes / Amidase signature (AS) domain / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chem-QJ9 / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMin, X. / Walker, N.P.C. / Wang, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Discovery and molecular basis of potent noncovalent inhibitors of fatty acid amide hydrolase (FAAH).
Authors: Min, X. / Thibault, S.T. / Porter, A.C. / Gustin, D.J. / Carlson, T.J. / Xu, H. / Lindstrom, M. / Xu, G. / Uyeda, C. / Ma, Z. / Li, Y. / Kayser, F. / Walker, N.P. / Wang, Z.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty-acid amide hydrolase 1
B: Fatty-acid amide hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,70328
Polymers129,1862
Non-polymers2,51726
Water12,538696
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint31 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.560, 104.720, 148.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Fatty-acid amide hydrolase 1 / Anandamide amidohydrolase 1 / Oleamide hydrolase 1


Mass: 64593.180 Da / Num. of mol.: 2 / Fragment: Residues 32-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Faah, Faah1 / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P97612, fatty acid amide hydrolase

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Non-polymers , 5 types, 722 molecules

#2: Chemical ChemComp-QJ9 / 1-{(3S)-1-[4-(1-benzofuran-2-yl)pyrimidin-2-yl]piperidin-3-yl}-3-ethyl-1,3-dihydro-2H-benzimidazol-2-one


Mass: 439.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25N5O2
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG3350, NH4F, pH 5.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: mirrors
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.383 Å / Num. all: 60454 / Num. obs: 60454 / % possible obs: 95 % / Redundancy: 5.2 % / Rsym value: 0.148 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.4250.4411.74325986380.44193.8
2.42-2.575.10.3632.14213182660.36394.9
2.57-2.755.20.292.64077078360.2995.5
2.75-2.975.30.2143.53860073280.21495.8
2.97-3.255.30.1484.93591767670.14895.9
3.25-3.645.30.1076.43267161530.10795.7
3.64-4.25.30.0877.52857653900.08795.4
4.2-5.145.30.07782423245860.07794.9
5.14-7.275.20.0867.41845935250.08693.6
7.27-49.524.90.0747.1956419650.07490.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2034 / WRfactor Rwork: 0.1668 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8827 / SU B: 5.222 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2915 / SU Rfree: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 3063 5.1 %RANDOM
Rwork0.1782 ---
obs0.1803 60331 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.03 Å2 / Biso mean: 17.1351 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8427 0 172 696 9295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228830
X-RAY DIFFRACTIONr_angle_refined_deg1.1932.00611954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10851117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55923.931346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.123151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5921556
X-RAY DIFFRACTIONr_chiral_restr0.0850.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216584
X-RAY DIFFRACTIONr_mcbond_it0.3091.55487
X-RAY DIFFRACTIONr_mcangle_it0.61228852
X-RAY DIFFRACTIONr_scbond_it1.03733343
X-RAY DIFFRACTIONr_scangle_it1.8134.53089
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 231 -
Rwork0.205 4104 -
all-4335 -
obs--93.05 %

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