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

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Basic information

Entry
Database: PDB / ID: 3qkv
TitleCrystal structure of fatty acid amide hydrolase with small molecule compound
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


Arachidonate metabolism / fatty acid amide hydrolase / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / monoacylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds ...Arachidonate metabolism / fatty acid amide hydrolase / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / fatty acid amide hydrolase activity / monoacylglycerol catabolic process / monoacylglycerol lipase activity / amidase activity / fatty acid catabolic process / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity, acting on ester bonds / positive regulation of vasoconstriction / organelle membrane / fatty acid metabolic process / phospholipid binding / presynapse / postsynapse / Golgi membrane / lipid binding / endoplasmic reticulum membrane / glutamatergic synapse / 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
Chem-QKV / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 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
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)129,8154
Polymers129,1862
Non-polymers6282
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-23 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.820, 104.080, 147.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-QKV / (6-bromo-1'H,4H-spiro[1,3-benzodioxine-2,4'-piperidin]-1'-yl)methanol


Mass: 314.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16BrNO3
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.52 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: ADSC / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→45.153 Å / Num. all: 26148 / Num. obs: 26148 / % possible obs: 100 % / Redundancy: 4.3 % / Rsym value: 0.234 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.274.30.4931.61624937580.493100
3.27-3.474.30.4091.81538435620.409100
3.47-3.714.30.2812.51440833390.281100
3.71-44.30.252.81346131210.25100
4-4.384.30.1963.81249328880.196100
4.38-4.94.30.1724.11134926320.172100
4.9-5.664.30.1913.81010223480.191100
5.66-6.934.30.2073.6854020050.207100
6.93-9.84.20.0917.7653115700.091100
9.8-45.1533.90.0688.435819250.06899.1

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MT5

1mt5


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.818 / Cor.coef. Fo:Fc free: 0.784 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.2428 / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8247 / SU B: 23.208 / SU ML: 0.399 / SU Rfree: 0.5338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2891 1327 5.1 %RANDOM
Rwork0.2665 ---
obs0.2676 26067 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 42.76 Å2 / Biso mean: 29.2197 Å2 / Biso min: 21.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---1.96 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8416 0 36 0 8452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0228671
X-RAY DIFFRACTIONr_angle_refined_deg0.8361.99811770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.39351098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82223.931346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02151492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7311556
X-RAY DIFFRACTIONr_chiral_restr0.050.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216502
X-RAY DIFFRACTIONr_mcbond_it0.0531.55455
X-RAY DIFFRACTIONr_mcangle_it0.09828790
X-RAY DIFFRACTIONr_scbond_it0.1433216
X-RAY DIFFRACTIONr_scangle_it0.1834.52976
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 82 -
Rwork0.307 1775 -
all-1857 -
obs--100 %

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