Research workbench
Molecular mechanism of MDGA1: regulation of neuroligin 2:NEUREXIN trans-synaptic bridges
Analyse Molecular mechanism of MDGA1: regulation of neuroligin 2:NEUREXIN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V5W
- Type
- protein
- Length
- 199 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mam domain-containing glycosylphosphatidylinositol anchor protein 1
- UniProt
- Q8NFP4
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mam domain-containing glycosylphosphatidylinositol anchor protein 1 | protein | 199 | 5% helix, 54% strand | Q8NFP4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.35 | 0.79 | 12 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5V5W · Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NFP4 · AlphaFold monomer V2.0 prediction for mam domain-containing glycosylphosphatidylinositol… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q8NFP4
- Elsewhere: RCSB PDB 5V5W · PDBe 5V5W · UniProt Q8NFP4
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