Research workbench
1.6 ångström crystal structure of the human neuroreceptor anchoring and molybdenum cofactor biosynthesis protein gephyrin
Analyse 1.6 ångström crystal structure of the human neuroreceptor anchoring and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JLJ
- Type
- protein
- Length
- 507 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gephyrin
- UniProt
- Q9NQX3
- Ligands
- NA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Gephyrin | protein | 169 | 48% helix, 19% strand | Q9NQX3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.78 | 0.88 | 41 | NA, FMT |
| 2 | 243 | 0.52 | 0.76 | 45 | empty |
| 3 | 231 | 0.52 | 0.76 | 37 | empty |
| 4 | 216 | 0.50 | 0.76 | 35 | empty |
| 5 | 65 | 0.34 | 0.76 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 789 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 788 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 787 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1JLJ · 1.6 Angstrom crystal structure of the human neuroreceptor anchoring and molybdenum… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NQX3 · AlphaFold monomer V2.0 prediction for gephyrin (Q9NQX3) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q9NQX3
- Elsewhere: RCSB PDB 1JLJ · PDBe 1JLJ · UniProt Q9NQX3
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