3TKD: GluA2 ligand-binding domain

Crystal structure of the GluA2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and cyclothiazide at 1.45 A resolution. Determined by X-ray diffraction at 1.45 Å resolution. Released 21 Sept 2011.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 4,982
Mol. weight: 60.42 kDa
Ligands: GLU, CYZ
Released: 21 Sept 2011

Explore 3TKD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TKD contains 33 α-helices and 40 β-strands across 2 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: 16 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	20	1
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	246-251	6
α-helix	252-256	5

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	8
β-strand	13	1	9
β-strand	17	1	9
β-strand	18-19	2	10
α-helix	20	1
α-helix	23-25	3
α-helix	28-31	4
β-strand	32-33	2	10
α-helix	35-47	13
β-strand	50-55	6	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	134-136	3	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	231-243	13
α-helix	246-254	9

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>3TKD_1 GLUTAMATE RECEPTOR 2 (chains A, B)
GANKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGK
YGARDADTKIWNGMVGELVYGKADIAIAPLTITYVREEVIDFSKPFMSLGISIMIKKGTP
IESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVAR
VRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGNAVNLAVLK
LSEQGLLDKLKNKWWYDKGECGS

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	2
CYZ	Cyclothiazide	C14 H16 Cl N3 O4 S2	2

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

Primary citation

Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2. Krintel, C., Frydenvang, K., Olsen, L. et al. Biochem J (2012) 441:173-178. DOI 10.1042/BJ20111221 · 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…

Browse structure collections

About this viewer

MolViewer shows 3TKD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.