3PMV | pdb_00003pmv

Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator

• PDB DOI: https://doi.org/10.2210/pdb3PMV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-18 Released: 2011-01-12 
• Deposition Author(s): Maclean, J.K.F., Jamieson, C., Brown, C.I., Campbell, R.A., Gillen, K.J., Gillespie, J., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Moir, E.M., Morrow, J.A., Pantling, J., Rankovic, Z., Smith, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Structure based evolution of a novel series of positive modulators of the AMPA receptor.

Jamieson, C., Maclean, J.K., Brown, C.I., Campbell, R.A., Gillen, K.J., Gillespie, J., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Moir, E.M., Morrow, J.A., Pantling, J., Rankovic, Z., Smith, L.

(2011) Bioorg Med Chem Lett 21: 805-811

• PubMed: 21190850 
• DOI: https://doi.org/10.1016/j.bmcl.2010.11.098
• Primary Citation Related Structures: 
  3PMV, 3PMW, 3PMX


• PubMed Abstract: 
  

  Starting from compound 1, we utilized biostructural data to successfully evolve an existing series into a new chemotype with a promising overall profile, exemplified by 19.

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Organizational Affiliation: 
• Merck Research Laboratories, MSD, Newhouse, Motherwell, Lanarkshire ML1 5SH, UK. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.58 kDa 
• Atom Count: 2,624 
• Modeled Residue Count: 263 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A	263	Rattus norvegicus	Mutation(s): 0  Gene Names: Gria2, Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
557	H [auth A]	N-[(2S)-2-{4-[4-(hydroxymethyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}propyl]propane-2-sulfonamide C17 H22 F3 N3 O3 S JXMBLTBPIRRCAZ-GFCCVEGCSA-N
GLU	B [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.22	α = 90
b = 87.23	β = 90
c = 47.4	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Maclean, J.K.F., Jamieson, C., Brown, C.I., Campbell, R.A., Gillen, K.J., Gillespie, J., Kazemier, B., Kiczun, M., Lamont, Y., Lyons, A.J., Moir, E.M., Morrow, J.A., Pantling, J., Rankovic, Z., Smith, L.

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-05-31
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary