Research workbench
X-ray structure of IGLUR5 ligand-binding core (S1S2) in complex with msviii-19 at 2.10A resolution
Analyse X-ray structure of IGLUR5 ligand-binding core (S1S2) in complex with msviii-19… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GBB
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- MS8
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 1 | protein | 255 | 36% helix, 22% strand | P22756 |
| B | Glutamate receptor, ionotropic kainate 1 | protein | 257 | 36% helix, 21% strand | P22756 |
Ligands and binding sites
- MS8 · (2R,3aR,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 901 | 0.78 | 0.81 | 97 | MS8 |
| 2 | 183 | 0.72 | 0.89 | 36 | MS8 |
| 3 | 141 | 0.43 | 0.75 | 27 | empty |
| 4 | 53 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 478 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3GBB · X-ray structure of iGluR5 ligand-binding core (S1S2) in complex with MSVIII-19 at 2.10A… · the same entry in another collection · chain B against B, TM-score 1.00
- P22756 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 1 (P22756) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P22756
- Elsewhere: RCSB PDB 3GBB · PDBe 3GBB · UniProt P22756
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.