Research workbench
Revisited crystal structure of NEUREXIN1BETA-NEUROLIGIN4 complex
Analyse Revisited crystal structure of NEUREXIN1BETA-NEUROLIGIN4 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XB6
- Type
- protein
- Length
- 1,424 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, CL
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuroligin-4, X-linked | protein | 529 | 37% helix, 16% strand | Q8N0W4 |
| B | Neuroligin-4, X-linked | protein | 541 | 36% helix, 16% strand | Q8N0W4 |
| C, D | Neurexin-1-beta | protein | 177 | 5% helix, 52% strand | Q63373 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains C, B, D
- CL · Chloride ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 30 copies · chains A, B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.73 | 0.98 | 19 | EDO |
| 2 | 60 | 0.73 | 0.98 | 18 | empty |
| 3 | 110 | 0.72 | 0.93 | 27 | empty |
| 4 | 176 | 0.70 | 0.88 | 35 | EDO |
| 5 | 451 | 0.64 | 0.77 | 51 | EDO, CL |
Interfaces
3 interfaces between chains.
- A–B · 801 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 656 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 650 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2XB6 · Revisited crystal structure of Neurexin1beta-Neuroligin4 complex · 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 2XB6 · PDBe 2XB6 · UniProt Q8N0W4 · UniProt Q63373
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