MolNFT v1 · #184068 · protein
Resting state GLUA1/A2 heterotetramer in complex with auxiliary subunit tarp gamma 8 (lbd-tmd)
7OCD · Isoform flip of glutamate receptor 1: “Resting state GLUA1/A2 heterotetramer in complex with auxiliary subunit tarp gamma 8 (lbd-tmd)”. Electron microscopy, 2 ligands (PC1, E2Q), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 7OCD
- Type
- protein
- Length
- 1,920 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform flip of glutamate receptor 1; Glutamate receptor 2; Voltage-dependent calcium…
- UniProt
- P19490, P19491, Q8VHW5
- Ligands
- PC1, E2Q
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isoform flip of glutamate receptor 1 | protein | 395 | 49% helix, 12% strand | P19490 |
| D, B | Glutamate receptor 2 | protein | 396 | 47% helix, 11% strand | P19491 |
| I, J | Voltage-dependent calcium channel gamma-8 subunit | protein | 169 | 63% helix, 8% strand | Q8VHW5 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 6 copies · chains A, B, C, D
- E2Q · 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide · ligand · 4 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.81 | 0.84 | 90 | empty |
| 2 | 1029 | 0.80 | 0.81 | 108 | empty |
| 3 | 148 | 0.79 | 0.96 | 19 | empty |
| 4 | 221 | 0.61 | 0.81 | 33 | empty |
| 5 | 240 | 0.60 | 0.80 | 34 | empty |
Interfaces
10 interfaces between chains.
- C–D · 2952 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2948 Ų buried · 16 hydrogen bonds · protein-protein
- C–B · 1984 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1982 Ų buried · 7 hydrogen bonds · protein-protein
- C–I · 762 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7OCD · Resting state GluA1/A2 heterotetramer in complex with auxiliary subunit TARP gamma 8… · the same entry in another collection · chain B against B, 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 0.97
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B against A, TM-score 0.91
- P19490 · AlphaFold monomer V2.0 prediction for glutamate receptor 1 (P19490) · a predicted model of the same protein · chain C against A, TM-score 0.66
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 Q8VHW5
- Elsewhere: RCSB PDB 7OCD · PDBe 7OCD · UniProt P19490 · UniProt P19491 · UniProt Q8VHW5
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