MolNFT v1 · #138297 · protein
GLUA2 bound to antagonist zk and GSG1L in digitonin, state 2
5WEL · Chimera of glutamate receptor 2, germ cell-specific gene 1…: “GLUA2 bound to antagonist zk and GSG1L in digitonin, state 2”. Electron microscopy, 2 ligands (ZK1, AJP), 20 pockets (best druggability 0.88). MolNFT v1 #138297 on…
- PDB
- 5WEL
- Type
- protein
- Length
- 3,484 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of glutamate receptor 2, germ cell-specific gene 1- like protein
- UniProt
- P19491, D3Z7H4
- Ligands
- ZK1, AJP
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Chimera of glutamate receptor 2, germ cell-specific gene 1- like protein | protein | 962 | 45% helix, 16% strand | P19491, D3Z7H4 |
| B, D | Chimera of glutamate receptor 2, germ cell-specific gene 1- like protein | protein | 780 | 41% helix, 18% strand | P19491, D3Z7H4 |
Ligands and binding sites
- 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
- AJP · Digitonin · 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 | 1084 | 0.88 | 0.89 | 130 | empty |
| 2 | 1046 | 0.85 | 0.86 | 130 | ZK1 |
| 3 | 1090 | 0.84 | 0.85 | 132 | ZK1 |
| 4 | 759 | 0.83 | 0.86 | 96 | empty |
| 5 | 494 | 0.83 | 0.90 | 90 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3650 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 3625 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 3124 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 3094 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 406 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5WEL · GluA2 bound to antagonist ZK and GSG1L in digitonin, state 2 · the same entry in another collection · chain A against A, TM-score 1.00
- D3Z7H4 · AlphaFold monomer V2.0 prediction for germ cell-specific gene 1-like protein (D3Z7H4) · a predicted model of the same protein · chain A against A, TM-score 0.18
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 D3Z7H4
- Elsewhere: RCSB PDB 5WEL · PDBe 5WEL · UniProt P19491 · UniProt D3Z7H4
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