3KS9

Metabotropic glutamate receptor mGluR1 complexed with LY341495 antagonist

• PDB DOI: https://doi.org/10.2210/pdb3KS9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


• Deposited: 2009-11-20 Released: 2009-12-08 
• Deposition Author(s): Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Bochkarev, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Metabotropic glutamate receptor mglur1 complexed with LY341495 antagonist

Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Bochkarev, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 112.58 kDa 
• Atom Count: 7,727 
• Modelled Residue Count: 887 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 1	A, B	496	Homo sapiens	Mutation(s): 1  Gene Names: GPRC1A, GRM1, MGLUR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13255 (Homo sapiens) Explore Q13255  Go to UniProtKB:  Q13255
PHAROS:  Q13255 GTEx:  ENSG00000152822
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q13255-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z99	C [auth A], G [auth B]	2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine C20 H19 N O5 VLZBRVJVCCNPRJ-KPHUOKFYSA-N
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Z99	BindingDB:  3KS9	Ki: 6800 (nM) from 1 assay(s)
		IC50: min: 7800, max: 8990 (nM) from 2 assay(s)
		EC50: 1.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.241 
• R-Value Work: 0.206 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.23	α = 90
b = 96.546	β = 106.67
c = 97.545	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Dobrovetsky, E., Khutoreskaya, G., Seitova, A., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Bochkarev, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references, Structure summary
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description