Research workbench
Nitrowillardiine bound to the ligand binding domain of GLUA2
Analyse Nitrowillardiine bound to the ligand binding domain of GLUA2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RTW
- Type
- protein
- Length
- 774 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- NWD, ZN
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F | Glutamate receptor 2 | protein | 258 | 37% helix, 21% strand | P19491 |
Ligands and binding sites
- NWD · 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine · ligand · 3 copies · chains B, D, F
- ZN · Zinc ion · metal · 5 copies · chains B, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.82 | 0.83 | 128 | empty |
| 2 | 59 | 0.70 | 0.97 | 18 | NWD |
| 3 | 52 | 0.69 | 0.97 | 18 | NWD |
| 4 | 51 | 0.69 | 0.98 | 18 | NWD |
| 5 | 271 | 0.58 | 0.78 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–D · 918 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 301 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3RTW · Nitrowillardiine bound to the ligand binding domain of GluA2 · the same entry in another collection · chain B against B, 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 3RTW · PDBe 3RTW · UniProt P19491
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