3LMK

Ligand Binding Domain of Metabotropoc glutamate receptor mGluR5 complexed with glutamate

• PDB DOI: https://doi.org/10.2210/pdb3LMK/pdb

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


• Deposited: 2010-01-30 Released: 2010-02-16 
• 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: 2.44 Å
• R-Value Free: 0.281 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Metabotropic Glutamate receptor mGluR5 complexed with glutamate

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.

Macromolecule Content

• Total Structure Weight: 111.69 kDa 
• Atom Count: 6,884 
• Modelled Residue Count: 877 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metabotropic glutamate receptor 5	A, B	492	Homo sapiens	Mutation(s): 1  Gene Names: GPRC1E, GRM5, MGLUR5
UniProt & NIH Common Fund Data Resources
Find proteins for P41594 (Homo sapiens) Explore P41594  Go to UniProtKB:  P41594
PHAROS:  P41594 GTEx:  ENSG00000168959
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P41594-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLU	D [auth A], I [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
MG	E [auth A], F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GLU	PDBBind:  3LMK	Ki: 1160 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.281 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.875	α = 90
b = 98.346	β = 90
c = 155.239	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
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: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement 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: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references, Structure summary
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary