Research workbench
Crystal structure of the chicken MDGA1 ectodomain
Analyse Crystal structure of the chicken MDGA1 ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OJ2
- Type
- protein
- Length
- 1,383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mam domain-containing glycosylphosphatidylinositol anchor protein 1
- UniProt
- Q0WYX8
- Ligands
- NAG, BMA, MAN
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mam domain-containing glycosylphosphatidylinositol anchor protein 1 | protein | 691 | 3% helix, 54% strand | Q0WYX8 |
| B | Mam domain-containing glycosylphosphatidylinositol anchor protein 1 | protein | 692 | 3% helix, 54% strand | Q0WYX8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.64 | 0.74 | 55 | empty |
| 2 | 242 | 0.61 | 0.81 | 39 | empty |
| 3 | 364 | 0.58 | 0.76 | 34 | empty |
| 4 | 182 | 0.58 | 0.81 | 30 | empty |
| 5 | 424 | 0.57 | 0.74 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 2835 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified, 17 glycan, 14 disulfide (engineered, N-glycosylation, disulfide).
Compared structures
- 5OJ2 · Crystal structure of the chicken MDGA1 ectodomain · the same entry in another collection · chain A against A, TM-score 1.00
- Q0WYX8 · AlphaFold monomer V2.0 prediction for mam domain-containing glycosylphosphatidylinositol… · a predicted model of the same protein · chain B 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 Q0WYX8
- Elsewhere: RCSB PDB 5OJ2 · PDBe 5OJ2 · UniProt Q0WYX8
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