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- PDB-4do3: Structure of FAAH with a non-steroidal anti-inflammatory drug -

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Basic information

Entry
Database: PDB / ID: 4do3
TitleStructure of FAAH with a non-steroidal anti-inflammatory drug
ComponentsFatty-acid amide hydrolase 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMIDASE / HYDROLASE / ANANDAMIDE / NSAID / DRUG / COX / INHIBITOR / INFLAMMATION / PAIN / 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 / organelle membrane / positive regulation of vasoconstriction / fatty acid metabolic process / phospholipid binding / presynapse / postsynapse / Golgi membrane / lipid binding / glutamatergic synapse / 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
(2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid / CYCLOHEXANE AMINOCARBOXYLIC ACID / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGarau, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: A Binding Site for Nonsteroidal Anti-inflammatory Drugs in Fatty Acid Amide Hydrolase.
Authors: Bertolacci, L. / Romeo, E. / Veronesi, M. / Magotti, P. / Albani, C. / Dionisi, M. / Lambruschini, C. / Scarpelli, R. / Cavalli, A. / De Vivo, M. / Piomelli, D. / Garau, G.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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

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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)126,6147
Polymers125,7452
Non-polymers8695
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-32 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.470, 104.370, 147.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 602
2114B1 - 602

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Components

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


Mass: 62872.398 Da / Num. of mol.: 2 / Fragment: UNP residues 32-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Faah, Faah1 / Production host: Escherichia coli (E. coli) / References: UniProt: P97612, fatty acid amide hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OHO / CYCLOHEXANE AMINOCARBOXYLIC ACID


Mass: 143.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO2
#4: Chemical ChemComp-0LA / (2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid / (S)-carprofen


Mass: 273.714 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12ClNO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 3.17 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG400, 100 MM TRIS-HCL, PH 7.5, 100 MM MGCL2, 100 MM NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287K, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.008 / Wavelength: 1.008 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.25→44.5 Å / Num. all: 76448 / Num. obs: 76403 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 11.6 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 15.9
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 4.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MOSFLMPACKAGEdata reduction
MOLREPphasing
REFMAC5.5.0109refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LJ7

3lj7


Resolution: 2.25→44.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.133 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.187 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19872 3838 5 %RANDOM
Rwork0.16439 ---
all0.16616 76448 --
obs0.16616 72435 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.831 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å2-0 Å2-0 Å2
2---1.37 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.25→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8369 0 57 533 8959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0228645
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.99911735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19451093
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24123.86342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.112151482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7931556
X-RAY DIFFRACTIONr_chiral_restr0.1320.21317
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216478
X-RAY DIFFRACTIONr_mcbond_it1.171.55436
X-RAY DIFFRACTIONr_mcangle_it2.13828758
X-RAY DIFFRACTIONr_scbond_it3.83133209
X-RAY DIFFRACTIONr_scangle_it6.1514.52973
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4216 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.260.5
MEDIUM THERMAL1.912
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 270 -
Rwork0.213 5293 -
obs--99.66 %

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