MolNFT v1 · #126433 · protein
Structure of GLUK1 ligand-binding domain (S1S2) in complex with (2S, 4R)-4-(2-CARBOXYPHENOXY)PYRROLIDINE-2-carboxylic acid at 3.18 a resolution
5M2V · Glutamate receptor ionotropic, kainate 1,GLUTAMATE receptor…: “Structure of GLUK1 ligand-binding domain (S1S2) in complex with (2S…”. X-ray diffraction, 3 ligands (7E5, SO4, CL), 3 pockets (best druggability 0.75). MolNFT v1 #126433…
- PDB
- 5M2V
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 1,GLUTAMATE receptor ionotropic, kainate 1
- UniProt
- P22756
- Ligands
- 7E5, SO4, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, kainate 1,GLUTAMATE receptor ionotropic, kainate 1 | protein | 251 | 39% helix, 21% strand | P22756 |
| B | Glutamate receptor ionotropic, kainate 1,GLUTAMATE receptor ionotropic, kainate 1 | protein | 253 | 39% helix, 21% strand | P22756 |
Ligands and binding sites
- 7E5 · (2~{S},4~{R})-4-(2-carboxyphenoxy)pyrrolidine-2-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.75 | 0.82 | 58 | 7E5 |
| 2 | 585 | 0.73 | 0.81 | 58 | 7E5 |
| 3 | 566 | 0.66 | 0.77 | 59 | SO4, CL |
Interfaces
1 interface between chains.
- A–B · 962 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5M2V · Structure of GluK1 ligand-binding domain (S1S2) in complex with… · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.97
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 5M2V · PDBe 5M2V · UniProt P22756
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