MolNFT v1 · #11402 · protein
1.6 ångström crystal structure of the human neuroreceptor anchoring and molybdenum cofactor biosynthesis protein gephyrin
1JLJ: “1.6 ångström crystal structure of the human neuroreceptor anchoring and molybdenum cofactor biosynthesis…”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.78). MolNFT v1 #11402 on GenesisL1: 3D structure, binding…
- 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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