Research workbench
Crystal structure of human MDGA1 and human neuroligin-2 complex
Analyse Crystal structure of human MDGA1 and human neuroligin-2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XEQ
- Type
- protein
- Length
- 817 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuroligin-2; Mam domain-containing glycosylphosphatidylinositol anchor protein 1
- UniProt
- Q8NFZ4, Q8NFP4
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuroligin-2 | protein | 525 | 35% helix, 16% strand | Q8NFZ4 |
| B | Mam domain-containing glycosylphosphatidylinositol anchor protein 1 | protein | 292 | 2% helix, 44% strand | Q8NFP4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.75 | 0.95 | 31 | empty |
| 2 | 451 | 0.71 | 0.81 | 49 | empty |
| 3 | 65 | 0.63 | 0.92 | 16 | empty |
| 4 | 320 | 0.59 | 0.77 | 43 | empty |
| 5 | 118 | 0.52 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1207 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5XEQ · Crystal Structure of human MDGA1 and human neuroligin-2 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NFZ4 · AlphaFold monomer V2.0 prediction for neuroligin-2 (Q8NFZ4) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8NFP4 · AlphaFold monomer V2.0 prediction for mam domain-containing glycosylphosphatidylinositol… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q8NFZ4
- Every structure of UniProt Q8NFP4
- Elsewhere: RCSB PDB 5XEQ · PDBe 5XEQ · UniProt Q8NFZ4 · UniProt Q8NFP4
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