MolNFT v1 · #77731 · protein
Crystal structure of IGLUR2 ligand binding domain with symmetric sulfonamide containing potentiator
3RNN · Glutamate receptor 2: “Crystal structure of IGLUR2 ligand binding domain with symmetric sulfonamide containing potentiator”. X-ray diffraction, 3 ligands (GLU, RNN, ZN), 5 pockets (best druggability 0.83). MolNFT v1 #77731 on…
- PDB
- 3RNN
- Type
- protein
- Length
- 776 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P42262
- Ligands
- GLU, RNN, ZN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor 2 | protein | 259 | 37% helix, 21% strand | P42262 |
| C | Glutamate receptor 2 | protein | 258 | 38% helix, 21% strand | P42262 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
- RNN · N,N'-(benzene-1,4-diyldiethane-2,1-diyl)dipropane-2-sulfonamide · ligand · 2 copies · chains A, C, B
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.83 | 0.84 | 133 | RNN |
| 2 | 282 | 0.58 | 0.78 | 29 | empty |
| 3 | 85 | 0.43 | 0.79 | 23 | empty |
| 4 | 84 | 0.40 | 0.78 | 20 | empty |
| 5 | 83 | 0.37 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 921 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 285 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3RNN · Crystal Structure of iGluR2 Ligand Binding Domain with Symmetric Sulfonamide Containing… · the same entry in another collection · chain A against A, TM-score 1.00
- P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P42262
- Elsewhere: RCSB PDB 3RNN · PDBe 3RNN · UniProt P42262
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