Research workbench
Complex GNGN2 of AMPA-subtype iglur GLUA2 in complex with auxiliary subunit GAMMA2 (stargazin) at low glutamate concentration (20 um) in the presence of cyclothiazide (100 um)
Analyse Complex GNGN2 of AMPA-subtype iglur GLUA2 in complex with auxiliary subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TNM
- Type
- protein
- Length
- 2,484 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform flip of glutamate receptor 2,VOLTAGE-dependent calcium channel gamma-3 subunit…
- UniProt
- P19491, Q8VHX0
- Ligands
- CYZ, GLU
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Isoform flip of glutamate receptor 2,VOLTAGE-dependent calcium channel gamma-3 subunit chimera | protein | 621 | 50% helix, 11% strand | P19491, Q8VHX0 |
| B, D | Isoform flip of glutamate receptor 2,VOLTAGE-dependent calcium channel gamma-3 subunit chimera | protein | 621 | 50% helix, 12% strand | P19491, Q8VHX0 |
Ligands and binding sites
- CYZ · Cyclothiazide · ligand · 4 copies · chains A, D, B, C
- GLU · Glutamic acid · ligand · 2 copies · chains A, C
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 | 934 | 0.84 | 0.85 | 113 | CYZ |
| 2 | 838 | 0.83 | 0.86 | 101 | empty |
| 3 | 1149 | 0.81 | 0.82 | 114 | CYZ |
| 4 | 934 | 0.81 | 0.83 | 81 | empty |
| 5 | 950 | 0.81 | 0.83 | 92 | empty |
Interfaces
4 interfaces between chains.
- B–C · 3719 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 3389 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2781 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 2705 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7TNM · Complex GNGN2 of AMPA-subtype iGluR GluA2 in complex with auxiliary subunit gamma2… · the same entry in another collection · chain B against B, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B against A, TM-score 0.62
- Q8VHX0 · AlphaFold monomer V2.0 prediction for voltage-dependent calcium channel gamma-3 subunit… · a predicted model of the same protein · chain C against A, TM-score 0.32
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 Q8VHX0
- Elsewhere: RCSB PDB 7TNM · PDBe 7TNM · UniProt P19491 · UniProt Q8VHX0
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