MolNFT v1 · #115173 · protein
Crystal structure of the GLUA2 ligand-binding domain (S1S2J) in complex with the antagonist (R)-2-amino-3-(3'-hydroxybiphenyl-3-yl) propanoic acid at 1.8A resolution
5CBS · Glutamate receptor 2,GLUTAMATE receptor 2: “Crystal structure of the GLUA2 ligand-binding domain (S1S2J) in complex with the antagonist…”. X-ray diffraction, 3 ligands (E42, SO4, CL), 11 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5CBS
- Type
- protein
- Length
- 1,042 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2,GLUTAMATE receptor 2
- UniProt
- P19491
- Ligands
- E42, SO4, CL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 260 | 38% helix, 21% strand | P19491 |
| B | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 259 | 38% helix, 21% strand | P19491 |
| C | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 261 | 38% helix, 21% strand | P19491 |
| D | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 262 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- E42 · (R)-2-amino-3-(3'-hydroxybiphenyl-3-yl)propanoic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.79 | 0.80 | 104 | E42, EDO, SO4 |
| 2 | 567 | 0.73 | 0.81 | 61 | E42, EDO |
| 3 | 692 | 0.72 | 0.78 | 74 | EDO, SO4 |
| 4 | 404 | 0.69 | 0.81 | 47 | E42, EDO |
| 5 | 423 | 0.69 | 0.81 | 45 | E42 |
Interfaces
4 interfaces between chains.
- A–C · 1117 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1106 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 656 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 274 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5CBS · Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
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 5CBS · PDBe 5CBS · UniProt P19491
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