6E5V | pdb_00006e5v

human mGlu8 receptor amino terminal domain in complex with (S)-3,4-Dicarboxyphenylglycine (DCPG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.306 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.255 (Depositor) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for ( S)-3,4-Dicarboxyphenylglycine (DCPG) As a Potent and Subtype Selective Agonist of the mGlu8Receptor.

Chen, Q.Ho, J.D.Ashok, S.Vargas, M.C.Wang, J.Atwell, S.Bures, M.Schkeryantz, J.M.Monn, J.A.Hao, J.

(2018) J Med Chem 61: 10040-10052

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01120
  • Primary Citation Related Structures: 
    6E5V

  • PubMed Abstract: 

    ( S)-3,4-Dicarboxyphenylglycine (DCPG) was first reported in 2001 as a potent orthosteric agonist with high subtype selectivity for the mGlu 8 receptor, but the structural basis for its high selectivity is not well understood. We have solved a cocrystal structure of recombinant human mGlu 8 amino terminal domain (ATD) protein bound to ( S)-DCPG, which possesses the largest lobe opening angle observed to date among known agonist-bound mGlu ATD crystal structures. The binding conformation of ( S)-DCPG observed in the crystal structure is significantly different from that in the homology model built from an l-glutamate-bound rat mGlu 1 ATD crystal structure, which has a smaller lobe opening angle. This highlights the importance of considering various lobe opening angles when modeling mGlu ATD-ligand complex. New homology models of other mGlu receptors based on the ( S)-DCPG-bound mGlu 8 ATD crystal structure were explored to rationalize ( S)-DCPG's high mGlu 8 receptor subtype selectivity.

Macromolecule Content 

  • Total Structure Weight: 118.21 kDa 
  • Atom Count: 6,754 
  • Modeled Residue Count: 882 
  • Deposited Residue Count: 1,046 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 8
A, B
523Homo sapiensMutation(s): 1 
Gene Names: GRM8GPRC1HMGLUR8
UniProt & NIH Common Fund Data Resources
Find proteins for O00222 (Homo sapiens)
Explore O00222 
Go to UniProtKB:  O00222
PHAROS:  O00222
GTEx:  ENSG00000179603 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00222
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.306 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.255 (Depositor) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.945α = 90
b = 106.78β = 90
c = 117.908γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary