MolNFT v1 · #95526 · protein
Crystal structure of the GLUA2 ligand-binding domain (S1S2J) in complex with the antagonist (2R)-ikm-159 at 2.3A resolution.
4ISU · Glutamate receptor 2: “Crystal structure of the GLUA2 ligand-binding domain (S1S2J) in complex with the antagonist (2R)-ikm-159 at…”. X-ray diffraction, 3 ligands (IKM, CL, SO4), 9 pockets (best druggability 0.80). MolNFT v1 #95526…
- PDB
- 4ISU
- Type
- protein
- Length
- 1,036 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- IKM, CL, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 258 | 38% helix, 22% strand | P19491 |
| D | Glutamate receptor 2 | protein | 260 | 39% helix, 21% strand | P19491 |
| C, B | Glutamate receptor 2 | protein | 259 | 37% helix, 20% strand | P19491 |
Ligands and binding sites
- IKM · (4aS,5aR,6R,8aS,8bS)-5a-(carboxymethyl)-8-oxo-2,4a,5a,6,7,8,8a,8b-octahydro-1H-pyrrolo[3',4':4,5]furo[3,2-b]pyridine-6-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, D, C, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.80 | 0.82 | 111 | CL, IKM |
| 2 | 825 | 0.80 | 0.83 | 99 | CL, SO4 |
| 3 | 339 | 0.66 | 0.81 | 46 | IKM |
| 4 | 200 | 0.62 | 0.83 | 34 | SO4 |
| 5 | 354 | 0.62 | 0.79 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1045 Ų buried · 11 hydrogen bonds · protein-protein
- D–B · 1022 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 522 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 222 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4ISU · 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 4ISU · PDBe 4ISU · UniProt P19491
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