Research workbench
Active state GLUA1/A2 AMPA receptor in complex with tarp gamma 8 and CNIH2 (lbd-tmd)
Analyse Active state GLUA1/A2 AMPA receptor in complex with tarp gamma 8 and CNIH2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OCF
- Type
- protein
- Length
- 2,294 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform flip of glutamate receptor 1; Isoform flip of glutamate receptor 2; Protein…
- UniProt
- P19490, P19491, Q5BJU5, Q8VHW5
- Ligands
- PC1, CYZ, GLU
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isoform flip of glutamate receptor 1 | protein | 406 | 47% helix, 10% strand | P19490 |
| B, D | Isoform flip of glutamate receptor 2 | protein | 399 | 45% helix, 10% strand | P19491 |
| G, E | Protein cornichon homolog 2 | protein | 158 | 77% helix, 0% strand | Q5BJU5 |
| I, J | Voltage-dependent calcium channel gamma-8 subunit | protein | 184 | 64% helix, 10% strand | Q8VHW5 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 26 copies · chains A, B, G, C, I, D, E, J
- CYZ · Cyclothiazide · ligand · 4 copies · chains A, B, C, D
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.80 | 0.82 | 111 | CYZ, GLU |
| 2 | 928 | 0.80 | 0.82 | 119 | CYZ, GLU |
| 3 | 689 | 0.76 | 0.82 | 54 | empty |
| 4 | 225 | 0.72 | 0.88 | 37 | empty |
| 5 | 67 | 0.71 | 0.96 | 19 | empty |
Interfaces
12 interfaces between chains.
- C–D · 2605 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2604 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 2017 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2016 Ų buried · 12 hydrogen bonds · protein-protein
- A–J · 874 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7OCF · Active state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD) · the same entry in another collection · chain D against D, TM-score 1.00
- Q8VHW5 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-8 subunit… · a predicted model of the same protein · chain I against A, TM-score 0.94
- Q5BJU5 · AlphaFold monomer V2.0 prediction for protein cornichon homolog 2 (Q5BJU5) · a predicted model of the same protein · chain G against A, TM-score 0.93
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 P19490
- Every structure of UniProt P19491
- Every structure of UniProt Q5BJU5
- Every structure of UniProt Q8VHW5
- Elsewhere: RCSB PDB 7OCF · PDBe 7OCF · UniProt P19490 · UniProt P19491 · UniProt Q5BJU5 · UniProt Q8VHW5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.