Research workbench
Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement
Analyse Crystal structure of synaptic protein neuroligin-4 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WQZ
- Type
- protein
- Length
- 1,443 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuroligin 4, X-linked; Neurexin-1-beta
- UniProt
- Q8N0W4, Q63373
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuroligin 4, X-linked | protein | 545 | 31% helix, 14% strand | Q8N0W4 |
| B | Neuroligin 4, X-linked | protein | 544 | 31% helix, 13% strand | Q8N0W4 |
| C, D | Neurexin-1-beta | protein | 177 | 4% helix, 46% strand | Q63373 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.71 | 0.82 | 57 | empty |
| 2 | 305 | 0.68 | 0.82 | 44 | empty |
| 3 | 208 | 0.64 | 0.83 | 35 | empty |
| 4 | 277 | 0.56 | 0.77 | 24 | empty |
| 5 | 305 | 0.56 | 0.76 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 818 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 634 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 612 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2WQZ · Crystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q63373 · AlphaFold monomer V2.0 prediction for neurexin-1-beta (Q63373) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q8N0W4 · AlphaFold monomer V2.0 prediction for neuroligin-4, X-linked (Q8N0W4) · 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 Q8N0W4
- Every structure of UniProt Q63373
- Elsewhere: RCSB PDB 2WQZ · PDBe 2WQZ · UniProt Q8N0W4 · UniProt Q63373
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