MolNFT v1 · #151602 · protein
Crystal structure of the ternary complex of gephe-ADP-glycine receptor derived peptide
6HSO · Gephyrin: “Crystal structure of the ternary complex of gephe-ADP-glycine receptor derived peptide”. X-ray diffraction, 4 ligands (ADP, 3F7, MG), 3 pockets (best druggability 0.46). MolNFT v1 #151602 on GenesisL1: 3D structure…
- PDB
- 6HSO
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gephyrin; Glycine receptor beta subunit derived peptide
- EC
- 2.7.7.75, 2.10.1.1
- UniProt
- Q03555
- Ligands
- ADP, 3F7, MG, PO4
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 412 | 21% helix, 34% strand | Q03555 |
| D, I | Glycine receptor beta subunit derived peptide | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- 3F7 · 1,1'-benzene-1,4-diylbis(1H-pyrrole-2,5-dione) · ligand · chains A, D, I
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- ACT · Acetate ion · additive · 6 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.46 | 0.77 | 23 | empty |
| 2 | 50 | 0.28 | 0.76 | 19 | MG, ADP |
| 3 | 50 | 0.28 | 0.75 | 10 | empty |
Interfaces
2 interfaces between chains.
- A–D · 679 Ų buried · 8 hydrogen bonds · protein-protein
- A–I · 153 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6HSO · Crystal structure of the ternary complex of GephE-ADP-Glycine receptor derived peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q03555 · AlphaFold monomer V2.0 prediction for gephyrin (Q03555) · 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 Q03555
- Elsewhere: RCSB PDB 6HSO · PDBe 6HSO · UniProt Q03555
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