MolNFT v1 · #116941 · protein
Crystal structure of the drosophila CG3822 KAIR1D ligand binding domain complex with glutamate
5DTB: “Crystal structure of the drosophila CG3822 KAIR1D ligand binding domain complex with glutamate”. X-ray diffraction, 2 ligands (GLU, NA), 4 pockets (best druggability 0.77). MolNFT v1 #116941 on GenesisL1: 3D structure, binding sites…
- 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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