5L1F

AMPA subtype ionotropic glutamate receptor GluA2 in complex with noncompetitive inhibitor Perampanel

• PDB DOI: https://doi.org/10.2210/pdb5L1F/pdb

• Classification: TRANSPORT PROTEIN/INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2016-07-29 Released: 2016-10-19 
• Deposition Author(s): Yelshanskaya, M.V., Singh, A.K., Sampson, J.M., Sobolevsky, A.I.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 361.51 kDa 
• Atom Count: 24,073 
• Modelled Residue Count: 3,100 
• Deposited Residue Count: 3,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2	A, B, C, D	803	Rattus norvegicus	Mutation(s): 4  Gene Names: Gria2, Glur2 Membrane Entity: Yes
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ZP	F [auth A], H [auth B], J [auth C], L [auth D]	2-(6'-oxo-1'-phenyl[1',6'-dihydro[2,3'-bipyridine]]-5'-yl)benzonitrile C23 H15 N3 O PRMWGUBFXWROHD-UHFFFAOYSA-N
NAG	E [auth A], G [auth B], I [auth C], K [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.237 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.74	α = 90
b = 109.345	β = 90
c = 594.835	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Yelshanskaya, M.V., Singh, A.K., Sampson, J.M., Sobolevsky, A.I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS083660

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary