MolNFT v1 · #187038 · protein
Structure of the complex of AMPA receptor GLUA2 with auxiliary subunit tarp gamma-5 bound to competitive antagonist zk 200775
7RZ4 · Glutamate receptor 2: “Structure of the complex of AMPA receptor GLUA2 with auxiliary subunit tarp gamma-5 bound to competitive…”. Electron microscopy, 3 ligands (PCW, ZK1, NAG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 7RZ4
- Type
- protein
- Length
- 3,574 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- PCW, ZK1, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 993 | 46% helix, 17% strand | P19491 |
| B, D | Glutamate receptor 2 | protein | 794 | 42% helix, 17% strand | P19491 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 24 copies · chains A, D, B, C
- ZK1 · {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 | 604 | 0.84 | 0.89 | 67 | empty |
| 2 | 837 | 0.83 | 0.85 | 110 | ZK1 |
| 3 | 1031 | 0.82 | 0.83 | 108 | empty |
| 4 | 1068 | 0.79 | 0.81 | 97 | empty |
| 5 | 1059 | 0.79 | 0.81 | 90 | empty |
Interfaces
6 interfaces between chains.
- C–D · 4263 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 4099 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 3237 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 3198 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 378 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7RZ4 · Structure of the complex of AMPA receptor GluA2 with auxiliary subunit TARP gamma-5 bound… · the same entry in another collection · chain D against D, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain C against A, TM-score 0.68
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
- Elsewhere: RCSB PDB 7RZ4 · PDBe 7RZ4 · UniProt P19491
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