Research workbench
Gephe in complex with para-phenyl crosslinked glycine receptor beta subunit derived dimeric peptide
Analyse Gephe in complex with para-phenyl crosslinked glycine receptor beta subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U91
- Type
- protein
- Length
- 437 residues
- Chains
- 3
- 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
- Ligands
- 3F7, CA
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gephyrin (EC 2.7.7.75, 2.10.1.1) | protein | 415 | 21% helix, 33% strand | Q03555 |
| B, E | Glycine receptor subunit beta | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- 3F7 · 1,1'-benzene-1,4-diylbis(1H-pyrrole-2,5-dione) · ligand · chains A, B, E
- CA · Calcium ion · metal · chains A
- ACT · Acetate ion · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
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 | 70 | 0.37 | 0.78 | 15 | empty |
| 2 | 60 | 0.30 | 0.75 | 15 | empty |
Interfaces
2 interfaces between chains.
- A–B · 673 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 148 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4U91 · GephE in complex with Para-Phenyl crosslinked Glycine receptor beta subunit derived… · 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 4U91 · PDBe 4U91 · UniProt Q03555
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