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Architecture and subunit arrangement of native AMPA receptors

Analyse Architecture and subunit arrangement of native AMPA receptors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NJM
Type: protein
Length: 5,420 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 3; Glutamate receptor 2; A'-C' auxiliary proteins; Voltage-dependent…
UniProt: P19492, P19491, Q71RJ2
Ligands: ZK1, NAG, BMA
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 8 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glutamate receptor 3	protein	784	43% helix, 17% strand	P19492
B, D	Glutamate receptor 2	protein	783	41% helix, 17% strand	P19491
E, G	A'-C' auxiliary proteins	protein	117	93% helix, 0% strand	—
F, H	Voltage-dependent calcium channel gamma-2 subunit	protein	169	69% helix, 9% strand	Q71RJ2
I, M	5B2 Fab light chain	protein	218	1% helix, 51% strand	—
J, N	5B2 Fab heavy chain	protein	213	7% helix, 54% strand	—
K, O	15F1 Fab light chain	protein	211	5% helix, 48% strand	—
L, P	15F1 Fab heavy chain	protein	215	1% helix, 52% strand	—

Ligands and binding sites

ZK1 · {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 4 copies

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	848	0.86	0.88	117	ZK1
2	990	0.83	0.84	102	ZK1
3	834	0.83	0.85	94	empty
4	488	0.82	0.88	66	empty
5	1192	0.81	0.82	143	empty

Interfaces

28 interfaces between chains.

A–B · 3483 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 3452 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 2815 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 2757 Å² buried · 10 hydrogen bonds · protein-protein
I–J · 733 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 glycan, 10 disulfide (disulfide, N-glycosylation, glycosylation).

Compared structures

6NJM · Architecture and subunit arrangement of native AMPA receptors · the same entry in another collection · chain P against P, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P19492
Every structure of UniProt P19491
Every structure of UniProt Q71RJ2
Elsewhere: RCSB PDB 6NJM · PDBe 6NJM · UniProt P19492 · UniProt P19491 · UniProt Q71RJ2

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