Research workbench
Crystal structure of the amino-terminal domain (atd) of iglur delta-2 (GLUD2)
Analyse Crystal structure of the amino-terminal domain (atd) of iglur delta-2 (GLUD2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KC8
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, delta-2
- UniProt
- O43424
- Ligands
- CA
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, delta-2 | protein | 398 | 39% helix, 22% strand | O43424 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.66 | 0.80 | 40 | EDO |
| 2 | 201 | 0.50 | 0.76 | 23 | empty |
| 3 | 98 | 0.42 | 0.78 | 21 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5KC8 · Crystal structure of the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2) · the same entry in another collection · chain A against A, TM-score 1.00
- O43424 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, delta-2 (O43424) · 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 O43424
- Elsewhere: RCSB PDB 5KC8 · PDBe 5KC8 · UniProt O43424
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