2E4Y

Crystal structure of the extracellular region of the group II metabotropic glutamate receptor complexed with 2R,4R-APDC

• PDB DOI: https://doi.org/10.2210/pdb2E4Y/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2006-12-17 Released: 2007-02-27 
• Deposition Author(s): Muto, T., Tsuchiya, D., Morikawa, K., Jingami, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 126.8 kDa 
• Atom Count: 7,823 
• Modelled Residue Count: 977 
• Deposited Residue Count: 1,110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 3	A, B	555	Rattus norvegicus	Mutation(s): 2
UniProt
Find proteins for P31422 (Rattus norvegicus) Explore P31422  Go to UniProtKB:  P31422

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
52A	D [auth A], E [auth B]	(2R,4R)-4-aminopyrrolidine-2,4-dicarboxylic acid C6 H10 N2 O4 XZFMJVJDSYRWDQ-AWFVSMACSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
52A	BindingDB:  2E4Y	Ki: 410 (nM) from 1 assay(s)
		EC50: min: 1700, max: 3000 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.393	α = 90
b = 91.799	β = 92.28
c = 112.972	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Muto, T., Tsuchiya, D., Morikawa, K., Jingami, H.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2021-11-10
  Changes: Advisory, Database references, Structure summary
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description