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- PDB-6mrg: FAAH bound to non covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 6mrg
TitleFAAH bound to non covalent inhibitor
ComponentsFatty-acid amide hydrolase 1
KeywordsHYDROLASE/INHIBITOR / Complex / 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-JXV / Fatty-acid amide hydrolase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsSaha, A. / Shih, A. / Mirzadegan, T. / Seierstad, M.
CitationJournal: J Chem Theory Comput / Year: 2018
Title: Predicting the Binding of Fatty Acid Amide Hydrolase Inhibitors by Free Energy Perturbation.
Authors: Saha, A. / Shih, A.Y. / Mirzadegan, T. / Seierstad, M.
History
DepositionOct 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)256,5158
Polymers255,1174
Non-polymers1,3984
Water25214
1
A: Fatty-acid amide hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1292
Polymers63,7791
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty-acid amide hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1292
Polymers63,7791
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fatty-acid amide hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1292
Polymers63,7791
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fatty-acid amide hydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1292
Polymers63,7791
Non-polymers3491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.208, 152.014, 299.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 63779.285 Da / Num. of mol.: 4
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-JXV / (1R)-2-{[6-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrimidin-4-yl]amino}-1-phenylethan-1-ol


Mass: 349.383 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H19N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: PEG8000, PHOSPHATE, PH 7.4

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0094 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0094 Å / Relative weight: 1
ReflectionResolution: 2.76→49.392 Å / Num. obs: 78055 / % possible obs: 92.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 64.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.35
Reflection shellResolution: 2.76→2.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.58 / Num. unique obs: 10777 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→49.392 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.65
RfactorNum. reflection% reflection
Rfree0.24 684 0.9 %
Rwork0.195 --
obs0.192 77327 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.77→49.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16727 0 104 14 16845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01117239
X-RAY DIFFRACTIONf_angle_d1.31923392
X-RAY DIFFRACTIONf_dihedral_angle_d11.36412461
X-RAY DIFFRACTIONf_chiral_restr0.062608
X-RAY DIFFRACTIONf_plane_restr0.0113023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.98380.32651590.278214994X-RAY DIFFRACTION91
2.9838-3.28410.31161220.2415586X-RAY DIFFRACTION94
3.2841-3.75910.23751150.204615410X-RAY DIFFRACTION93
3.7591-4.73550.24231500.168815320X-RAY DIFFRACTION92
4.7355-49.39950.20671380.170315333X-RAY DIFFRACTION90
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.12750.0133-0.22521.60370.88960.3380.1737-0.4249-0.54260.15790.92621.25130.0562-0.91090.2433-0.11370.2415-0.4058-0.8743-0.7284-25.46167.880842.9683
20.7513-0.0086-0.14560.87220.11630.7947-0.1158-0.0263-0.9171-0.0806-0.0906-0.03650.27350.64430.1875-0.2546-0.0813-0.6456-1.0748-0.2053-8.5993-25.902423.8413
31.6278-0.0339-0.42671.0507-0.12020.6101-0.02990.0902-0.3123-0.0357-0.0152-0.0840.00710.01730.308-0.11150.10930.3482-0.15130.36268.835947.397131.7691
40.99130.0226-0.13150.74870.18471.03260.1022-0.24620.18390.2218-0.06140.3287-0.2745-0.15880.3928-0.02710.17360.3762-0.17360.4188-26.000862.75750.1674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 32:574 )A32 - 574
2X-RAY DIFFRACTION2( CHAIN B AND RESID 33:574 )B33 - 574
3X-RAY DIFFRACTION3( CHAIN C AND RESID 33:574 )C33 - 574
4X-RAY DIFFRACTION4( CHAIN D AND RESID 33:574 )D33 - 574

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