MolNFT v1 · #169976 · protein
Crystal structure of GLUA2 AMPA receptor in complex with trans-4- butylcyclohexane carboxylic acid (4-bcca) inhibitor
6XSR · Glutamate receptor 2: “Crystal structure of GLUA2 AMPA receptor in complex with trans-4- butylcyclohexane carboxylic acid (4-bcca)…”. X-ray diffraction, 2 ligands (V8G, NAG), 20 pockets (best druggability 0.85). MolNFT v1 #169976 on…
- PDB
- 6XSR
- Type
- protein
- Length
- 3,088 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- V8G, NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 770 | 38% helix, 18% strand | P19491 |
| B, D | Glutamate receptor 2 | protein | 772 | 36% helix, 17% strand | P19491 |
| C | Glutamate receptor 2 | protein | 774 | 39% helix, 17% strand | P19491 |
Ligands and binding sites
- V8G · trans-4-butylcyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.85 | 0.88 | 95 | empty |
| 2 | 475 | 0.76 | 0.84 | 37 | empty |
| 3 | 338 | 0.75 | 0.87 | 48 | empty |
| 4 | 104 | 0.75 | 0.95 | 27 | empty |
| 5 | 83 | 0.72 | 0.96 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3500 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 3419 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 2958 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2704 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 372 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 6XSR · Crystal structure of GluA2 AMPA receptor in complex with trans-4-butylcyclohexane… · the same entry in another collection · chain D against D, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 6XSR · PDBe 6XSR · UniProt P19491
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