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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: 5VOV
Type: protein
Length: 2,274 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 0.80

Structure

electron microscopy · 4 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Glutamate receptor 2	protein	400	50% helix, 14% strand	P19491
B, D	Glutamate receptor 2	protein	402	49% helix, 13% 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	166	70% helix, 10% strand	Q71RJ2

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1121	0.80	0.82	127	empty
2	730	0.80	0.84	104	empty
3	973	0.80	0.81	125	empty
4	545	0.76	0.83	88	empty
5	175	0.76	0.92	33	empty

Interfaces

12 interfaces between chains.

B–C · 717 Å² buried · 1 hydrogen bond · protein-protein
A–D · 714 Å² buried · 1 hydrogen bond · protein-protein
C–D · 557 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 546 Å² buried · 0 hydrogen bonds · protein-protein
A–F · 227 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5VOV · Structure of AMPA receptor-TARP complex · the same entry in another collection · chain H against H, 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 5VOV · PDBe 5VOV · UniProt P19491 · UniProt Q71RJ2

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