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The structure of the ligand-binding domain of neurexin 1BETA: regulation of lns domain function by alternative splicing
Analyse The structure of the ligand-binding domain of neurexin 1BETA: regulation of lns… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C4R
- Type
- protein
- Length
- 1,433 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurexin-I beta
- UniProt
- Q63373
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neurexin-I beta | protein | 180 | 5% helix, 51% strand | Q63373 |
| B, D | Neurexin-I beta | protein | 178 | 6% helix, 52% strand | Q63373 |
| E | Neurexin-I beta | protein | 181 | 7% helix, 51% strand | Q63373 |
| F, H | Neurexin-I beta | protein | 177 | 5% helix, 53% strand | Q63373 |
| G | Neurexin-I beta | protein | 182 | 7% helix, 51% strand | Q63373 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.79 | 0.81 | 116 | empty |
| 2 | 655 | 0.74 | 0.80 | 77 | empty |
| 3 | 1144 | 0.73 | 0.77 | 119 | empty |
| 4 | 82 | 0.39 | 0.78 | 18 | empty |
| 5 | 69 | 0.35 | 0.77 | 15 | empty |
Interfaces
11 interfaces between chains.
- A–B · 505 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 483 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 473 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 432 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 431 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1C4R · The structure of the ligand-binding domain of neurexin 1BETA: regulation of lns domain… · the same entry in another collection · chain H against H, TM-score 1.00
- Q63373 · AlphaFold monomer V2.0 prediction for neurexin-1-beta (Q63373) · a predicted model of the same protein · chain F 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 Q63373
- Elsewhere: RCSB PDB 1C4R · PDBe 1C4R · UniProt Q63373
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