Research workbench
Nitrowillardiine bound to the ligand binding domain of GLUA2 at pH 3.5
Analyse Nitrowillardiine bound to the ligand binding domain of GLUA2 at pH 3.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q30
- Type
- protein
- Length
- 774 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2 chimeric protein
- UniProt
- P19491
- Ligands
- NWD, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, F | Glutamate receptor 2 chimeric protein | protein | 258 | 38% 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.83 | 0.84 | 140 | empty |
| 2 | 53 | 0.69 | 0.97 | 20 | NWD |
| 3 | 55 | 0.69 | 0.97 | 18 | NWD |
| 4 | 298 | 0.60 | 0.79 | 32 | empty |
| 5 | 139 | 0.42 | 0.75 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–D · 864 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 316 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 73 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4Q30 · Nitrowillardiine bound to the ligand binding domain of GluA2 at pH 3.5 · 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 4Q30 · PDBe 4Q30 · UniProt P19491
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