MolNFT v1 · #38502 · protein
Crystal structure of the second LNS/LG domain from neurexin 1 alpha
2H0B · Neurexin-1-alpha: “Crystal structure of the second LNS/LG domain from neurexin 1 alpha”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.52). MolNFT v1 #38502 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2H0B
- Type
- protein
- Length
- 727 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurexin-1-alpha
- UniProt
- Q28146
- Ligands
- CA
- Pockets
- 8 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurexin-1-alpha | protein | 181 | 6% helix, 54% strand | Q28146 |
| C | Neurexin-1-alpha | protein | 183 | 5% helix, 52% strand | Q28146 |
| D | Neurexin-1-alpha | protein | 182 | 5% helix, 53% strand | Q28146 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.52 | 0.85 | 17 | empty |
| 2 | 175 | 0.52 | 0.79 | 31 | empty |
| 3 | 83 | 0.45 | 0.81 | 18 | empty |
| 4 | 88 | 0.44 | 0.80 | 14 | empty |
| 5 | 108 | 0.42 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 574 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 341 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 262 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
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 Q28146
- Elsewhere: RCSB PDB 2H0B · PDBe 2H0B · UniProt Q28146
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