MolNFT v1 · #103315 · protein
Structure of gephyrin E domain with glycine-beta receptor peptide
4PD1: “Structure of gephyrin E domain with glycine-beta receptor peptide”. X-ray diffraction, 2 pockets (best druggability 0.34). MolNFT v1 #103315 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PD1
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gephyrin; Glycine receptor subunit beta
- EC
- 2.7.7.75, 2.10.1.1
- UniProt
- Q03555, P20781
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 404 | 21% helix, 34% strand | Q03555 |
| C | Glycine receptor subunit beta | protein | 10 | 0% helix, 0% strand | P20781 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.34 | 0.78 | 14 | empty |
| 2 | 52 | 0.28 | 0.75 | 10 | GOL |
Interfaces
1 interface between chains.
- A–C · 693 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4PD1 · Structure of gephyrin E domain with Glycine-beta receptor 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
- P20781 · AlphaFold monomer V2.0 prediction for glycine receptor subunit beta (P20781) · a predicted model of the same protein · chain C against A, TM-score 0.46
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
- Every structure of UniProt P20781
- Elsewhere: RCSB PDB 4PD1 · PDBe 4PD1 · UniProt Q03555 · UniProt P20781
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