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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: 5VOT
Type: protein
Length: 2,322 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 0.84

Structure

electron microscopy · 4 distinct chains · 53% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glutamate receptor 2	protein	408	49% helix, 14% strand	P19491
D, B	Glutamate receptor 2	protein	409	46% helix, 14% strand	P19491
E, G	Voltage-dependent calcium channel gamma-2 subunit	protein	169	67% helix, 8% strand	Q71RJ2
F, H	Voltage-dependent calcium channel gamma-2 subunit	protein	175	67% helix, 9% 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	938	0.84	0.85	141	empty
2	210	0.77	0.91	33	empty
3	640	0.75	0.81	85	empty
4	543	0.74	0.82	85	empty
5	587	0.74	0.81	74	empty

Interfaces

14 interfaces between chains.

C–B · 2447 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 2431 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1891 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 1882 Å² buried · 6 hydrogen bonds · protein-protein
C–H · 753 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5VOT · Structure of AMPA receptor-TARP complex · the same entry in another collection · chain B against B, 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 0.96

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 5VOT · PDBe 5VOT · UniProt P19491 · UniProt Q71RJ2

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