Research workbench
Crystal structure of GLUA2 T625G, con-ikot-ikot snail toxin, partial agonist ka and postitive modulator (R,R)-2B complex
Analyse Crystal structure of GLUA2 T625G, con-ikot-ikot snail toxin, partial agonist ka… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U5E
- Type
- protein
- Length
- 3,135 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2; Con-ikot-ikot
- UniProt
- P19491, P0CB20
- Ligands
- KAI, FWF, NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 738 | 42% helix, 19% strand | P19491 |
| B | Glutamate receptor 2 | protein | 743 | 41% helix, 19% strand | P19491 |
| C | Glutamate receptor 2 | protein | 746 | 42% helix, 19% strand | P19491 |
| D | Glutamate receptor 2 | protein | 738 | 41% helix, 19% strand | P19491 |
| E, F | Con-ikot-ikot | protein | 85 | 56% helix, 0% strand | P0CB20 |
Ligands and binding sites
- KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 4 copies · chains A, B, C, D
- FWF · N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide · ligand · 2 copies · chains A, D, B, C
- 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 | 885 | 0.84 | 0.86 | 126 | KAI, FWF |
| 2 | 904 | 0.81 | 0.83 | 73 | empty |
| 3 | 610 | 0.81 | 0.86 | 80 | FWF |
| 4 | 933 | 0.79 | 0.81 | 82 | empty |
| 5 | 1071 | 0.78 | 0.80 | 123 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2645 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2470 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 2093 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 2055 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 953 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4U5E · Crystal structure of GluA2 T625G, con-ikot-ikot snail toxin, partial agonist KA and… · the same entry in another collection · chain F against F, TM-score 1.00
- P0CB20 · AlphaFold monomer V2.0 prediction for con-ikot-ikot (P0CB20) · a predicted model of the same protein · chain F against A, TM-score 0.96
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain A against A, TM-score 0.74
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 P0CB20
- Elsewhere: RCSB PDB 4U5E · PDBe 4U5E · UniProt P19491 · UniProt P0CB20
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