MolNFT v1 · #104186 · protein
Nitrowillardiine bound to the ligand binding domain of GLUA2 at pH 3.5
4Q30 · Glutamate receptor 2 chimeric protein: “Nitrowillardiine bound to the ligand binding domain of GLUA2 at pH 3.5”. X-ray diffraction, 2 ligands (NWD, ZN), 8 pockets (best druggability 0.83). MolNFT v1 #104186 on GenesisL1: 3D…
- 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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