MolNFT v1 · #118098 · protein
Gephe in complex with MG(2+) - AMP
5ERS · Gephyrin: “Gephe in complex with MG(2+) - AMP”. X-ray diffraction, 3 ligands (AMP, MG, PO4), 5 pockets (best druggability 0.42). MolNFT v1 #118098 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ERS
- Type
- protein
- Length
- 414 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
- AMP, MG, PO4
- Pockets
- 5 · best druggability 0.42
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 | 414 | 21% helix, 33% strand | Q03555 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.42 | 0.76 | 21 | empty |
| 2 | 59 | 0.33 | 0.77 | 22 | AMP, MG |
| 3 | 71 | 0.33 | 0.74 | 16 | MPD |
| 4 | 73 | 0.32 | 0.75 | 17 | empty |
| 5 | 59 | 0.31 | 0.75 | 16 | empty |
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 5ERS · PDBe 5ERS · UniProt Q03555
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