MolNFT v1 · #187039 · protein
Structure of the complex of lbd-tmd part of AMPA receptor GLUA2 with auxiliary subunit tarp gamma-5 bound to competitive antagonist zk 200775
7RZ5 · Glutamate receptor 2: “Structure of the complex of lbd-tmd part of AMPA receptor GLUA2 with auxiliary subunit tarp gamma-5 bound to…”. Electron microscopy, 2 ligands (PCW, ZK1), 20 pockets (best druggability 0.83). MolNFT v1 #187039…
- PDB
- 7RZ5
- Type
- protein
- Length
- 2,046 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- PCW, ZK1
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor 2 | protein | 611 | 52% helix, 14% strand | P19491 |
| B, D | Glutamate receptor 2 | protein | 412 | 46% helix, 16% 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
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 | 803 | 0.83 | 0.86 | 88 | empty |
| 2 | 298 | 0.83 | 0.94 | 25 | empty |
| 3 | 668 | 0.82 | 0.86 | 78 | empty |
| 4 | 637 | 0.72 | 0.79 | 55 | empty |
| 5 | 432 | 0.71 | 0.82 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–D · 3377 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 3358 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 2907 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 2799 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7RZ5 · Structure of the complex of LBD-TMD part of AMPA receptor GluA2 with auxiliary subunit… · 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 B against A, TM-score 0.91
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 7RZ5 · PDBe 7RZ5 · UniProt P19491
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