Molecular mechanism of activation of the immunoregulatory amidase NAAA.

Gorelik, A.; Gebai, A.; Illes, K.; Piomelli, D.; Nagar, B.

doi:10.2210/pdb6dy3/pdb

Macromolecule Content

Total Structure Weight: 161482.61
Atom Count: 11007
Residue Count: 1388
Unique protein chains: 2

6DY3

Caenorhabditis elegans N-acylethanolamine-hydrolyzing acid amidase (NAAA) ortholog

DOI: 10.2210/pdb6DY3/pdb

Classification: HYDROLASE
Organism(s): Caenorhabditis elegans
Expression System: Spodoptera frugiperda

Deposited: 2018-07-01 Released: 2018-09-26
Deposition Author(s): Gorelik, A., Gebai, A., Illes, K., Piomelli, D., Nagar, B.
Funding Organization(s): Canadian Institutes of Health Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.7 Å
R-Value Free: 0.215
R-Value Work: 0.168

wwPDB Validation3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Molecular mechanism of activation of the immunoregulatory amidase NAAA.

Gorelik, A., Gebai, A., Illes, K., Piomelli, D., Nagar, B.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E10032-E10040

PubMed: 30301806 Search on PubMed
Primary Citation of Related Structures:
6DY2, 6DY1, 6DY0, 6DXZ, 6DXY, 6DXX, 6DXW

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
N-acylethanolamine-hydrolyzing acid amidase alpha-subunit	A, C, E, G	113	Caenorhabditis elegans	Mutation(s): 0 EC: 3.5.1.-
Find proteins for Q9GUI1 (Caenorhabditis elegans) Go to UniProtKB: Q9GUI1
Protein Feature View Full Protein Feature View for Q9GUI1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
N-acylethanolamine-hydrolyzing acid amidase beta-subunit	B, D, F, H	234	Caenorhabditis elegans	Mutation(s): 0 EC: 3.5.1.-
Find proteins for Q9GUI1 (Caenorhabditis elegans) Go to UniProtKB: Q9GUI1
Protein Feature View Full Protein Feature View for Q9GUI1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
FUC Query on FUC Download SDF File Download CCD File	B, F	ALPHA-L-FUCOSE C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Ligand Interaction
NAG Query on NAG Download SDF File Download CCD File	B, F	N-ACETYL-D-GLUCOSAMINE C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.7 Å
R-Value Free: 0.215
R-Value Work: 0.168
Space Group: P 4₃

Unit Cell:

Length (Å)	Angle (°)
a = 89.614	α = 90.00
b = 89.614	β = 90.00
c = 207.058	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-07-01
Released Date: 2018-09-26
Deposition Author(s): Gorelik, A., Gebai, A., Illes, K., Piomelli, D., Nagar, B.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research	Canada	MOP-133535

Revision History

Version 1.0: 2018-09-26
Type: Initial release
Version 1.1: 2018-10-10
Type: Data collection, Database references, Structure summary
Version 1.2: 2018-10-24
Type: Data collection, Database references, Structure summary
Version 1.3: 2018-11-07
Type: Data collection, Database references
Version 1.4: 2019-04-17
Type: Data collection, Structure summary

Prepare Data

Validate Data

Deposit Data

Deposition Help & Resources

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6DY3

Caenorhabditis elegans N-acylethanolamine-hydrolyzing acid amidase (NAAA) ortholog

Molecular mechanism of activation of the immunoregulatory amidase NAAA.

Entity ID: 1

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History