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Crystal structure of the GLUR2 ligand binding core (HS1S2J) in complex with cnqx at 2.5 a resolution
Analyse Crystal structure of the GLUR2 ligand binding core (HS1S2J) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B7D
- Type
- protein
- Length
- 2,063 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- CNI
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, H | Glutamate receptor 2 | protein | 258 | 36% helix, 22% strand | P19491 |
| C, G | Glutamate receptor 2 | protein | 257 | 37% helix, 23% strand | P19491 |
| D | Glutamate receptor 2 | protein | 259 | 36% helix, 23% strand | P19491 |
Ligands and binding sites
- CNI · 7-nitro-2,3-dioxo-2,3-dihydroquinoxaline-6-carbonitrile · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.83 | 0.85 | 129 | CNI |
| 2 | 1165 | 0.81 | 0.82 | 135 | CNI |
| 3 | 1106 | 0.77 | 0.79 | 115 | CNI |
| 4 | 1017 | 0.77 | 0.79 | 113 | CNI |
| 5 | 529 | 0.73 | 0.81 | 52 | CNI |
Interfaces
10 interfaces between chains.
- E–F · 975 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 961 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 957 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 950 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 510 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3B7D · Crystal structure of the GLUR2 ligand binding core (HS1S2J) in complex with CNQX at 2.5 A… · 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 3B7D · PDBe 3B7D · UniProt P19491
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