6YK4: AMPA receptor GluA2o ligand-binding domain

Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound ( S) - 1- [2'-Amino-2'-carboxyethyl]-6-methyl-5 ,7- dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 1.00A. Determined by X-ray diffraction at 1.0 Å resolution. Released 3 Jun 2020.

Method: X-ray diffraction
Resolution: 1.0 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 2,771
Mol. weight: 30.36 kDa
Ligands: CG8, LI
Released: 3 Jun 2020

Explore 6YK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YK4 contains 14 α-helices and 20 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	13	1	2
β-strand	17	1	2
β-strand	18-19	2	3
α-helix	23-25	3
α-helix	28-31	4
β-strand	32-33	2	3
α-helix	35-47	13
β-strand	51-55	5	1
β-strand	64	1	4
β-strand	71	1	4
α-helix	73-79	7
β-strand	85-86	2	1
β-strand	91	1	5
α-helix	94-97	4
β-strand	100-102	3	1
α-helix	103	1
α-helix	105	1
β-strand	107-109	3	5
β-strand	111-116	6	6
α-helix	124-128	5
β-strand	134-136	3	6
β-strand	138	1	7
α-helix	142-149	8
α-helix	153-164	12
β-strand	171	1	7
α-helix	174-183	10
β-strand	188-193	6	6
α-helix	194-201	8
β-strand	208-211	4	6
β-strand	218-220	3	5
β-strand	223-225	3	1
α-helix	231-243	13
α-helix	246-255	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 2,Glutamate receptor 2	A	protein	264	Rattus norvegicus	P19491 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YK4_1 Glutamate receptor 2,Glutamate receptor 2 (chains A)
GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGK
YGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTP
IESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVAR
VRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLK
LNEQGLLDKLKNKWWYDKGECGSG

Ligands and cofactors

ID	Name	Formula	Copies
CG8	(2~{S})-2-azanyl-3-[6-methyl-2,4-bis(oxidanylidene)-5,7-dihydropyrrolo[3,4-d]py…	C10 H14 N4 O4	1
LI	Lithium ion	Li	1

Water and common crystallization additives (CL, GOL, SO4) are not listed.

Primary citation

Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions. Frydenvang, K., Pickering, D.S., Kshirsagar, G.U. et al. ACS Chem Neurosci (2020) 11:1791-1800. DOI 10.1021/acschemneuro.0c00195 · PubMed

Other PDB entries of the same protein (UniProt P19491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NG9 1.15 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
6YK5 1.15 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
6YK3 1.2 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5JEI 1.23 Å, Crystal structure of the GluA2 LBD in complex with FW
4IGT 1.24 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist…
4YU0 1.26 Å, Crystal structure of a tetramer of GluA2 TR mutant ligand binding domains bound with…
5NIH 1.3 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
1MQI 1.35 Å, Crystal Structure of the GluR2 Ligand Binding Core (S1S2J) in Complex with…
5FTI 1.35 Å, Crystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (lithium form)
4U21 1.39 Å, GluA2flip sLBD complexed with FW and (R,R)-2b crystal form E
4FAT 1.4 Å, Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an…
6FAZ 1.4 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the…

Browse structure collections

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