Research workbench
Crystal structure of the drosophila CG3822 KAIR1D ligand binding domain complex with glutamate
Analyse Crystal structure of the drosophila CG3822 KAIR1D ligand binding domain complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DTB
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG3822
- UniProt
- Q9VDH5
- Ligands
- GLU, NA
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CG3822 | protein | 263 | 37% helix, 23% strand | Q9VDH5 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.77 | 0.80 | 109 | GOL |
| 2 | 56 | 0.58 | 0.91 | 19 | empty |
| 3 | 73 | 0.34 | 0.75 | 21 | empty |
| 4 | 71 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 838 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5DTB · Crystal structure of the Drosophila CG3822 KaiR1D ligand binding domain complex with… · the same entry in another collection · chain A against A, 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 Q9VDH5
- Elsewhere: RCSB PDB 5DTB · PDBe 5DTB · UniProt Q9VDH5
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