Research workbench
Structural basis of dynamic glycine receptor clustering
Analyse Structural basis of dynamic glycine receptor clustering in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T3E
- Type
- protein
- Length
- 822 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gephyrin; 49-mer fragment of glycine receptor beta chain
- UniProt
- Q03555, P20781
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gephyrin | protein | 412 | 20% helix, 32% strand | Q03555 |
| B | Gephyrin | protein | 405 | 20% helix, 27% strand | Q03555 |
| P | 49-mer fragment of glycine receptor beta chain | protein | 5 | 0% helix, 0% strand | P20781 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.80 | 0.83 | 72 | SO4 |
| 2 | 562 | 0.80 | 0.86 | 63 | SO4 |
| 3 | 546 | 0.79 | 0.86 | 69 | empty |
| 4 | 809 | 0.76 | 0.80 | 69 | SO4 |
| 5 | 112 | 0.69 | 0.92 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3599 Ų buried · 34 hydrogen bonds · protein-protein
- B–P · 307 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1T3E · Structural basis of dynamic glycine receptor clustering · 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 B against A, TM-score 0.97
- P20781 · AlphaFold monomer V2.0 prediction for glycine receptor subunit beta (P20781) · a predicted model of the same protein · chain P against A, TM-score 0.82
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 1T3E · PDBe 1T3E · UniProt Q03555 · UniProt P20781
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