[English] 日本語
Yorodumi
- PDB-6dxz: Rabbit N-acylethanolamine-hydrolyzing acid amidase (NAAA) in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / N-acylethanolamine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process ...N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / N-acylethanolamine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process / fatty acid metabolic process / lysosome / membrane
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
4-(2,4,4-trimethylpentan-2-yl)phenol / : / Chem-TON / Chem-WTF / N-acylethanolamine-hydrolyzing acid amidase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
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 / Item: _entity.pdbx_ec
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-acylethanolamine acid amidase alpha-subunit
B: N-acylethanolamine acid amidase beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,51610
Polymers38,3812
Non-polymers2,1358
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-15 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.143, 159.143, 159.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

-
Components

-
N-acylethanolamine acid amidase ... , 2 types, 2 molecules AB

#1: Protein N-acylethanolamine acid amidase alpha-subunit


Mass: 12124.106 Da / Num. of mol.: 1 / Fragment: residues 3-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: G1T7U7, N-(long-chain-acyl)ethanolamine deacylase
#2: Protein N-acylethanolamine acid amidase beta-subunit


Mass: 26256.689 Da / Num. of mol.: 1 / Fragment: CBAH domain residues 99-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: G1T7U7, N-(long-chain-acyl)ethanolamine deacylase

-
Sugars , 1 types, 2 molecules

#3: 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.: 2
Source method: isolated from a genetically manipulated source
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

-
Non-polymers , 6 types, 166 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE / Triton X-100


Mass: 352.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#6: Chemical ChemComp-27L / 4-(2,4,4-trimethylpentan-2-yl)phenol


Mass: 206.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22O
#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.: 1 / Source method: obtained synthetically / Formula: C21H22FN3O3S2
#8: Chemical ChemComp-TON / 2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL


Mass: 294.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.89 %
Crystal growMethod: vapor diffusion / Details: 0.2 M tripotassium citrate with 20 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 19528 / % possible obs: 100 % / Redundancy: 71.9 % / Net I/σ(I): 38.5
Reflection shellResolution: 2.7→2.8 Å

-
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→45.941 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 1917 10 %
Rwork0.1816 --
obs0.1856 19162 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 145 160 2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042851
X-RAY DIFFRACTIONf_angle_d0.7833909
X-RAY DIFFRACTIONf_dihedral_angle_d11.1281650
X-RAY DIFFRACTIONf_chiral_restr0.046423
X-RAY DIFFRACTIONf_plane_restr0.004483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.76760.28591020.2521918X-RAY DIFFRACTION75
2.7676-2.84240.31081360.22321227X-RAY DIFFRACTION100
2.8424-2.9260.25981350.22271216X-RAY DIFFRACTION100
2.926-3.02040.25741360.21691232X-RAY DIFFRACTION100
3.0204-3.12840.24831380.20881230X-RAY DIFFRACTION100
3.1284-3.25360.20341380.19241240X-RAY DIFFRACTION100
3.2536-3.40160.26681360.1881232X-RAY DIFFRACTION100
3.4016-3.58090.21011370.16681230X-RAY DIFFRACTION100
3.5809-3.80520.20771370.16591241X-RAY DIFFRACTION100
3.8052-4.09880.18891420.14471264X-RAY DIFFRACTION100
4.0988-4.51090.16471390.13861262X-RAY DIFFRACTION100
4.5109-5.16290.16121410.13981264X-RAY DIFFRACTION100
5.1629-6.50180.22961440.18621303X-RAY DIFFRACTION100
6.5018-45.94730.2781560.22891386X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more