1M5E: GLUR2 ligand binding core

X-ray structure of the GLUR2 ligand binding core (S1S2J) in complex with acpa at 1.46 a resolution. Determined by X-ray diffraction at 1.46 Å resolution. Released 18 Sept 2002.

Method: X-ray diffraction
Resolution: 1.46 Å
Organism: Rattus norvegicus
Chains: 3
Atoms: 7,182
Mol. weight: 88.89 kDa
Ligands: AM1, ZN
Released: 18 Sept 2002

Explore 1M5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1M5E contains 52 α-helices and 60 β-strands across 3 chains. 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: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5	1
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
α-helix	90	1
β-strand	91	1	5
α-helix	92	1
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	124-129	6
β-strand	134-137	4	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	194-200	7
β-strand	208-211	4	6
β-strand	218-220	3	5
β-strand	223-225	3	1
α-helix	230-243	14
α-helix	246-251	6
α-helix	252-257	6

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	8
β-strand	13	1	9
β-strand	17	1	9
β-strand	18-19	2	10
α-helix	20	1
α-helix	29-31	3
β-strand	32-33	2	10
α-helix	35-47	13
β-strand	51-55	5	8
β-strand	64	1	11
β-strand	71	1	11
α-helix	73-79	7
β-strand	85-86	2	8
α-helix	90	1
β-strand	91	1	12
α-helix	92	1
α-helix	94-97	4
β-strand	100-102	3	8
α-helix	103	1
α-helix	105	1
β-strand	107-109	3	12
β-strand	111-116	6	13
α-helix	124-128	5
β-strand	134-137	4	13
β-strand	138	1	14
α-helix	142-149	8
α-helix	153-164	12
β-strand	171	1	14
α-helix	174-183	10
β-strand	188-193	6	13
α-helix	194-201	8
β-strand	208-211	4	13
β-strand	218-220	3	12
β-strand	223-225	3	8
α-helix	231-244	14
α-helix	246-251	6
α-helix	252-256	5

Chain C: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	15
β-strand	13	1	16
β-strand	17	1	16
β-strand	18-19	2	17
α-helix	23-25	3
α-helix	28-31	4
β-strand	32-33	2	17
α-helix	35-47	13
β-strand	51-55	5	15
β-strand	64	1	18
β-strand	71	1	18
α-helix	73-79	7
β-strand	85-86	2	15
α-helix	90	1
β-strand	91	1	19
α-helix	92	1
α-helix	94-97	4
β-strand	100-102	3	15
α-helix	103	1
α-helix	105	1
β-strand	107-109	3	19
β-strand	111-116	6	20
α-helix	124-128	5
β-strand	134-137	4	20
β-strand	138	1	21
α-helix	142-149	8
α-helix	153-164	12
β-strand	171	1	21
α-helix	174-183	10
β-strand	188-193	6	20
α-helix	194-200	7
β-strand	208-211	4	20
β-strand	218-220	3	19
β-strand	223-225	3	15
α-helix	230-243	14
α-helix	246-251	6
α-helix	252-256	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 2	A, B, C	protein	263	Rattus norvegicus	P19491 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>1M5E_1 Glutamate receptor 2 (chains A, B, C)
GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGK
YGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKGTP
IESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVAR
VRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLK
LNEQGLLDKLKNKWWYDKGECGS

Ligands and cofactors

ID	Name	Formula	Copies
AM1	(s)-2-amino-3-(3-carboxy-5-methylisoxazol-4-yl)propionic acid	C8 H10 N2 O5	3
ZN	Zinc ion	Zn	8

Water and common crystallization additives (ACT) are not listed.

Primary citation

Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 Ligand-binding Core. Hogner, A., Kastrup, J.S., Jin, R. et al. J Mol Biol (2002) 322:93-109. DOI 10.1016/S0022-2836(02)00650-2 · PubMed

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

6YK4 1.0 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
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…

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