MolNFT v1 · #148766 · protein
Crystal structure of gephyrin E domain in complex with artemether
6FGD: “Crystal structure of gephyrin E domain in complex with artemether”. X-ray diffraction, 5 ligands (ADP, D8Z, CA), 4 pockets (best druggability 0.38). MolNFT v1 #148766 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FGD
- Type
- protein
- Length
- 413 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gephyrin
- EC
- 2.7.7.75, 2.10.1.1
- UniProt
- Q03555
- Ligands
- ADP, D8Z, CA, NA, PO4
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 413 | 21% helix, 33% strand | Q03555 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- D8Z · Artemether · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 24 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.38 | 0.75 | 22 | empty |
| 2 | 87 | 0.35 | 0.74 | 16 | D8Z |
| 3 | 62 | 0.29 | 0.74 | 11 | empty |
| 4 | 54 | 0.27 | 0.75 | 22 | CA, ADP |
Compared structures
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 Q03555
- Elsewhere: RCSB PDB 6FGD · PDBe 6FGD · UniProt Q03555
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