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Structure of AMPA receptor-tarp complex

Analyse Structure of AMPA receptor-tarp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5VOU
Type: protein
Length: 2,326 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutamate receptor 2; Voltage-dependent calcium channel gamma-2 subunit
UniProt: P19491, Q71RJ2
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 4 distinct chains · 54% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glutamate receptor 2	protein	409	49% helix, 13% strand	P19491
D, B	Glutamate receptor 2	protein	410	47% helix, 13% strand	P19491
E, G	Voltage-dependent calcium channel gamma-2 subunit	protein	169	69% helix, 9% strand	Q71RJ2
H, F	Voltage-dependent calcium channel gamma-2 subunit	protein	175	67% helix, 4% strand	Q71RJ2

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	1064	0.83	0.84	104	empty
2	836	0.78	0.82	117	empty
3	574	0.77	0.84	81	empty
4	183	0.77	0.92	36	empty
5	702	0.76	0.81	88	empty

Interfaces

14 interfaces between chains.

C–B · 2297 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 2296 Å² buried · 6 hydrogen bonds · protein-protein
D–C · 1685 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1683 Å² buried · 6 hydrogen bonds · protein-protein
H–C · 637 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5VOU · Structure of AMPA receptor-TARP complex · the same entry in another collection · chain F against F, TM-score 1.00
Q71RJ2 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-2 subunit… · a predicted model of the same protein · chain E against A, TM-score 0.95

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 P19491
Every structure of UniProt Q71RJ2
Elsewhere: RCSB PDB 5VOU · PDBe 5VOU · UniProt P19491 · UniProt Q71RJ2

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