MolNFT v1 · #129410 · protein
Crystal structure of the human neuroligin 1 cholinesterase domain containing spliced sequence B (ssb) (NL1(-A+B))
5OJK · Neuroligin-1,NEUROLIGIN-1: “Crystal structure of the human neuroligin 1 cholinesterase domain containing spliced sequence B (ssb)…”. X-ray diffraction, 1 ligand (NAG), 13 pockets (best druggability 0.70). MolNFT v1 #129410 on…
- PDB
- 5OJK
- Type
- protein
- Length
- 1,074 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuroligin-1,NEUROLIGIN-1
- UniProt
- Q8N2Q7
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuroligin-1,NEUROLIGIN-1 | protein | 537 | 37% helix, 15% strand | Q8N2Q7 |
| B | Neuroligin-1,NEUROLIGIN-1 | protein | 537 | 37% helix, 15% strand | Q8N2Q7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.70 | 0.83 | 48 | empty |
| 2 | 365 | 0.69 | 0.82 | 47 | empty |
| 3 | 62 | 0.66 | 0.94 | 20 | empty |
| 4 | 55 | 0.64 | 0.94 | 19 | empty |
| 5 | 299 | 0.56 | 0.76 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 826 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5OJK · Crystal structure of the human neuroligin 1 cholinesterase domain containing spliced… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N2Q7 · AlphaFold monomer V2.0 prediction for neuroligin-1 (Q8N2Q7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8N2Q7
- Elsewhere: RCSB PDB 5OJK · PDBe 5OJK · UniProt Q8N2Q7
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