3KG2: AMPA subtype ionotropic glutamate receptor

AMPA subtype ionotropic glutamate receptor in complex with competitive antagonist ZK 200775. Determined by X-ray diffraction at 3.6 Å resolution. Released 8 Dec 2009.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 22,686
Mol. weight: 372.48 kDa
Ligands: ZK1
Released: 8 Dec 2009

Explore 3KG2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KG2 contains 143 α-helices and 152 β-strands across 4 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: 35 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-19	9	1
α-helix	23-35	13
β-strand	42-50	9	1
α-helix	55-67	13
β-strand	72-75	4	1
α-helix	82-91	10
β-strand	95-98	4	1
α-helix	101-103	3
β-strand	110-112	3	1
α-helix	115-116	2
α-helix	118-127	10
β-strand	132-137	6	2
α-helix	139-141	3
α-helix	144-155	12
β-strand	159-164	6	2
α-helix	180-183	4
β-strand	191-195	5	2
α-helix	198-211	14
β-strand	215	1	3
β-strand	219-222	4	2
β-strand	226	1	2
β-strand	239	1	3
β-strand	241-246	6	2
α-helix	253-262	10
α-helix	280-300	21
α-helix	325-333	9
β-strand	339-340	2	4
β-strand	343-344	2	4
β-strand	347	1	5
β-strand	353	1	5
β-strand	357-363	7	2
β-strand	368-375	8	2
β-strand	379-382	4	2
β-strand	395-399	5	6
β-strand	407-408	2	7
α-helix	412-414	3
α-helix	417-420	4
β-strand	421-422	2	7
α-helix	424-436	13
β-strand	440-444	5	6
β-strand	453	1	8
β-strand	460	1	8
α-helix	462-468	7
β-strand	474-475	2	6
β-strand	480	1	9
α-helix	483-486	4
β-strand	489-491	3	6
α-helix	492	1
α-helix	494	1
β-strand	496-498	3	9
β-strand	500-505	6	10
α-helix	506-507	2
α-helix	514-516	3
α-helix	523-537	15
α-helix	540-542	3
α-helix	569-579	11
α-helix	596-629	34
α-helix	637-641	5
β-strand	646-648	3	10
β-strand	650	1	11
α-helix	654-661	8
α-helix	665-676	12
β-strand	683	1	11
α-helix	686-694	9
β-strand	700-705	6	10
α-helix	706-713	8
β-strand	720-723	4	10
β-strand	730-732	3	9
β-strand	735-737	3	6
α-helix	743-755	13
α-helix	758-764	7
α-helix	765-769	5
α-helix	790-816	27

Chain B: 35 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-19	9	12
α-helix	23-35	13
β-strand	42-50	9	12
α-helix	55-67	13
β-strand	72-75	4	12
α-helix	82-91	10
β-strand	95-98	4	12
α-helix	101-103	3
β-strand	110-112	3	12
α-helix	115-116	2
α-helix	118-127	10
β-strand	132-137	6	13
α-helix	139-141	3
α-helix	144-155	12
β-strand	159-164	6	13
α-helix	180-183	4
β-strand	191-195	5	13
α-helix	198-211	14
β-strand	215	1	14
β-strand	219-222	4	13
β-strand	226	1	13
β-strand	239	1	14
β-strand	241-246	6	13
α-helix	253-262	10
α-helix	280-300	21
α-helix	325-333	9
β-strand	339-340	2	15
β-strand	343-344	2	15
β-strand	347	1	16
β-strand	353	1	16
β-strand	357-363	7	13
β-strand	368-375	8	13
β-strand	379-382	4	13
β-strand	395-399	5	17
β-strand	407-408	2	18
α-helix	412-414	3
α-helix	417-420	4
β-strand	421-422	2	18
α-helix	424-436	13
β-strand	440-444	5	17
β-strand	453	1	19
β-strand	460	1	19
α-helix	462-468	7
β-strand	474-475	2	17
β-strand	480	1	20
α-helix	483-486	4
β-strand	489-491	3	17
α-helix	492	1
α-helix	494	1
β-strand	496-498	3	20
β-strand	500-505	6	21
α-helix	514-516	3
α-helix	523-537	15
α-helix	540-542	3
α-helix	569-579	11
α-helix	596-625	30
α-helix	637-641	5
β-strand	646-648	3	21
β-strand	650	1	22
α-helix	654-661	8
α-helix	665-676	12
β-strand	683	1	22
α-helix	686-694	9
β-strand	700-705	6	21
α-helix	706-713	8
β-strand	720-723	4	21
β-strand	730-732	3	20
β-strand	735-737	3	17
α-helix	743-755	13
α-helix	758-764	7
α-helix	765-769	5
α-helix	775-778	4
α-helix	790-816	27

Chain C: 36 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-19	9	23
α-helix	23-35	13
β-strand	42-50	9	23
α-helix	55-67	13
β-strand	72-75	4	23
α-helix	82-91	10
β-strand	95-98	4	23
α-helix	101-103	3
β-strand	110-112	3	23
α-helix	115-116	2
α-helix	118-127	10
β-strand	132-137	6	24
α-helix	139-141	3
α-helix	144-155	12
β-strand	159-164	6	24
α-helix	180-183	4
β-strand	191-195	5	24
α-helix	198-211	14
β-strand	215	1	25
β-strand	219-222	4	24
β-strand	226	1	24
β-strand	239	1	25
β-strand	241-246	6	24
α-helix	253-262	10
α-helix	280-300	21
α-helix	325-333	9
β-strand	339-340	2	26
β-strand	343-344	2	26
β-strand	347	1	27
β-strand	353	1	27
β-strand	357-363	7	24
β-strand	368-375	8	24
β-strand	379-382	4	24
α-helix	393-394	2
β-strand	395-399	5	28
β-strand	407-408	2	29
α-helix	412-414	3
α-helix	417-420	4
β-strand	421-422	2	29
α-helix	424-436	13
β-strand	440-444	5	28
β-strand	453	1	30
β-strand	460	1	30
α-helix	462-468	7
β-strand	474-475	2	28
β-strand	480	1	31
α-helix	483-486	4
β-strand	489-491	3	28
α-helix	492	1
α-helix	494	1
β-strand	496	1	31
β-strand	500-505	6	32
α-helix	514-516	3
α-helix	523-537	15
α-helix	540-542	3
α-helix	569-579	11
α-helix	596-629	34
α-helix	637-641	5
β-strand	646-648	3	32
β-strand	650	1	33
α-helix	654-661	8
α-helix	665-676	12
β-strand	683	1	33
α-helix	686-694	9
β-strand	700-705	6	32
α-helix	706-713	8
β-strand	720-723	4	32
β-strand	732	1	31
β-strand	735-737	3	28
α-helix	743-755	13
α-helix	758-764	7
α-helix	765-769	5
α-helix	775-778	4
α-helix	790-816	27

Chain D: 37 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	11-19	9	34
α-helix	23-35	13
β-strand	42-50	9	34
α-helix	55-67	13
β-strand	72-75	4	34
α-helix	82-91	10
β-strand	95-98	4	34
α-helix	101-103	3
β-strand	110-112	3	34
α-helix	115-116	2
α-helix	118-127	10
β-strand	132-137	6	35
α-helix	139-141	3
α-helix	144-155	12
β-strand	159-164	6	35
α-helix	180-183	4
β-strand	191-195	5	35
α-helix	198-211	14
β-strand	215	1	36
β-strand	219-222	4	35
β-strand	226	1	35
β-strand	239	1	36
β-strand	241-246	6	35
α-helix	253-262	10
α-helix	280-300	21
α-helix	325-333	9
β-strand	339-340	2	37
β-strand	343-344	2	37
β-strand	347	1	38
β-strand	353	1	38
β-strand	357-363	7	35
β-strand	368-375	8	35
β-strand	379-382	4	35
α-helix	388-390	3
α-helix	393-394	2
β-strand	395-399	5	39
β-strand	407-408	2	40
α-helix	412-414	3
α-helix	417-420	4
β-strand	421-422	2	40
α-helix	424-436	13
β-strand	440-444	5	39
β-strand	453	1	41
β-strand	460	1	41
α-helix	462-468	7
β-strand	474-475	2	39
β-strand	480	1	42
α-helix	483-486	4
β-strand	489-491	3	39
α-helix	492	1
α-helix	494	1
β-strand	496-498	3	42
β-strand	500-505	6	43
α-helix	514-516	3
α-helix	523-537	15
α-helix	540-542	3
α-helix	569-579	11
α-helix	596-625	30
α-helix	637-641	5
β-strand	646-648	3	43
β-strand	650	1	44
α-helix	654-661	8
α-helix	665-676	12
β-strand	683	1	44
α-helix	686-694	9
β-strand	700-705	6	43
α-helix	706-713	8
β-strand	720-723	4	43
β-strand	730-732	3	42
β-strand	735-737	3	39
α-helix	743-755	13
α-helix	758-764	7
α-helix	765-769	5
α-helix	775-778	4
α-helix	790-816	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 2	A, B, C, D	protein	823	Rattus norvegicus	P19491 (AlphaFold model)

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

>3KG2_1 Glutamate receptor 2 (chains A, B, C, D)
NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRG
VYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGALLSLIEYYQ
WDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKE
RRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVD
YDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR
GNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPR
KIGYWSEVDKMVLTEDDTSGLEQKTVVVTTILESPYVMMKANHAALAGNERYEGYCVDLA
AEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVI
DFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPY
EWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGADISPRSLSGRIVGGVWWFFT
LIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDK
MWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDS
KGYGIATPKGSSLGTPVNLAVLKLSEQGLLDKLKNKWWYDKGECGAKDSGSKEKTSALSL
SNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKGLVPRG

Ligands and cofactors

ID	Name	Formula	Copies
ZK1	{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl…	C14 H15 F3 N3 O6 P	4

Primary citation

X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor. Sobolevsky, A.I., Rosconi, M.P., Gouaux, E. Nature (2009) 462:745-756. DOI 10.1038/nature08624 · 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 more

3KG2 is part of these collections:

About this viewer

MolViewer shows 3KG2 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.