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- PDB-6dxx: Human N-acylethanolamine-hydrolyzing acid amidase (NAAA) in compl... -

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Basic information

Entry
Database: PDB / ID: 6dxx
TitleHuman N-acylethanolamine-hydrolyzing acid amidase (NAAA) in complex with non-covalent benzothiazole-piperazine inhibitor ARN19702, in presence of Triton X-100
Components(N-acylethanolamine-hydrolyzing acid amidase subunit ...) x 2
KeywordsHYDROLASE / endocannabinoid / lipase
Function / homology
Function and homology information


Neurotransmitter release cycle / N-(long-chain-acyl)ethanolamine deacylase / N-(long-chain-acyl)ethanolamine deacylase activity / N-acylethanolamine metabolic process / sphingosine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity ...Neurotransmitter release cycle / N-(long-chain-acyl)ethanolamine deacylase / N-(long-chain-acyl)ethanolamine deacylase activity / N-acylethanolamine metabolic process / sphingosine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / extrinsic component of membrane / lipid catabolic process / lysosomal lumen / fatty acid metabolic process / DNA-binding transcription factor binding / lysosome / extracellular exosome / cytoplasm
Similarity search - Function
Acid ceramidase-like / Acid ceramidase, N-terminal / beta subunit of N-acylethanolamine-hydrolyzing acid amidase / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family
Similarity search - Domain/homology
THIOCYANATE ION / Chem-TON / Chem-WTF / N-acylethanolamine-hydrolyzing acid amidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Molecular mechanism of activation of the immunoregulatory amidase NAAA.
Authors: Gorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B.
History
DepositionJul 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.3Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Apr 17, 2019Group: Data collection / Structure summary / Category: entity / struct / Item: _entity.pdbx_ec / _struct.pdbx_descriptor
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
B: N-acylethanolamine-hydrolyzing acid amidase subunit beta
C: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
D: N-acylethanolamine-hydrolyzing acid amidase subunit beta
E: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
F: N-acylethanolamine-hydrolyzing acid amidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,49336
Polymers115,9626
Non-polymers4,53030
Water3,603200
1
A: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
B: N-acylethanolamine-hydrolyzing acid amidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,36910
Polymers38,6542
Non-polymers1,7158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-61 kcal/mol
Surface area13690 Å2
MethodPISA
2
C: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
D: N-acylethanolamine-hydrolyzing acid amidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,26116
Polymers38,6542
Non-polymers1,60714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-94 kcal/mol
Surface area13560 Å2
MethodPISA
3
E: N-acylethanolamine-hydrolyzing acid amidase subunit alpha
F: N-acylethanolamine-hydrolyzing acid amidase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,86210
Polymers38,6542
Non-polymers1,2088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-53 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.610, 99.798, 92.756
Angle α, β, γ (deg.)90.00, 96.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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N-acylethanolamine-hydrolyzing acid amidase subunit ... , 2 types, 6 molecules ACEBDF

#1: Protein N-acylethanolamine-hydrolyzing acid amidase subunit alpha / Acid ceramidase-like protein / N-acylsphingosine amidohydrolase-like / ASAH-like protein


Mass: 12318.347 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAAA, ASAHL, PLT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q02083, N-(long-chain-acyl)ethanolamine deacylase
#2: Protein N-acylethanolamine-hydrolyzing acid amidase subunit beta / Acid ceramidase-like protein / N-acylsphingosine amidohydrolase-like / ASAH-like protein


Mass: 26335.783 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAAA, ASAHL, PLT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q02083, N-(long-chain-acyl)ethanolamine deacylase

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Sugars , 2 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 224 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-TON / 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL


Mass: 294.429 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C18H30O3
#7: Chemical ChemComp-WTF / [2-(ethylsulfonyl)phenyl][(2S)-4-(6-fluoro-1,3-benzothiazol-2-yl)-2-methylpiperazin-1-yl]methanone


Mass: 447.546 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C21H22FN3O3S2
#8: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M NaSCN and 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.69 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.69 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 37978 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 5.5
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U7Z

5u7z


Resolution: 2.7→46.113 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 3316 5.74 %
Rwork0.2056 --
obs0.208 57819 77.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7827 0 281 200 8308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058343
X-RAY DIFFRACTIONf_angle_d0.78311400
X-RAY DIFFRACTIONf_dihedral_angle_d11.7174851
X-RAY DIFFRACTIONf_chiral_restr0.0471252
X-RAY DIFFRACTIONf_plane_restr0.0051442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.73870.406370.3774616X-RAY DIFFRACTION21
2.7387-2.77950.4943450.3354793X-RAY DIFFRACTION27
2.7795-2.8230.3696630.30591055X-RAY DIFFRACTION36
2.823-2.86920.3217790.29791218X-RAY DIFFRACTION42
2.8692-2.91870.3206860.28951381X-RAY DIFFRACTION47
2.9187-2.97180.3248960.29691565X-RAY DIFFRACTION54
2.9718-3.02890.30191040.27771830X-RAY DIFFRACTION62
3.0289-3.09070.28071260.27882067X-RAY DIFFRACTION69
3.0907-3.15790.28421400.26962184X-RAY DIFFRACTION75
3.1579-3.23140.32251370.26682343X-RAY DIFFRACTION80
3.2314-3.31220.31491450.24732478X-RAY DIFFRACTION84
3.3122-3.40170.29711540.22062591X-RAY DIFFRACTION88
3.4017-3.50170.26911620.22082655X-RAY DIFFRACTION90
3.5017-3.61470.25471740.20742750X-RAY DIFFRACTION94
3.6147-3.74390.23341680.19862844X-RAY DIFFRACTION96
3.7439-3.89370.26691750.18652898X-RAY DIFFRACTION99
3.8937-4.07080.23011820.18232962X-RAY DIFFRACTION99
4.0708-4.28530.17941770.1692916X-RAY DIFFRACTION100
4.2853-4.55350.18671810.15392932X-RAY DIFFRACTION99
4.5535-4.90480.19451800.15582903X-RAY DIFFRACTION99
4.9048-5.39770.20031780.17582946X-RAY DIFFRACTION99
5.3977-6.17710.25291750.20922917X-RAY DIFFRACTION99
6.1771-7.77650.2871790.22172915X-RAY DIFFRACTION99
7.7765-46.11990.23411730.19622744X-RAY DIFFRACTION93

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