Research workbench
Crystal structure of unliganded myorg
Analyse Crystal structure of unliganded myorg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QQF
- Type
- protein
- Length
- 2,427 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myogenesis-regulating glycosidase
- EC
- 3.2.1.-
- UniProt
- Q6NSJ0
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 612 | 26% helix, 28% strand | Q6NSJ0 |
| B | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 616 | 26% helix, 28% strand | Q6NSJ0 |
| C | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 618 | 26% helix, 28% strand | Q6NSJ0 |
| D | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 581 | 27% helix, 26% strand | Q6NSJ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 31 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C
- MAN · alpha-D-mannopyranose · sugar
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- MLI · Malonate ion · additive · 4 copies · chains A, B, C, 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 | 138 | 0.69 | 0.89 | 26 | ACT |
| 2 | 128 | 0.68 | 0.89 | 20 | ACT |
| 3 | 125 | 0.68 | 0.89 | 19 | ACT |
| 4 | 132 | 0.68 | 0.89 | 21 | ACT |
| 5 | 312 | 0.61 | 0.79 | 46 | empty |
Interfaces
3 interfaces between chains.
- B–C · 705 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 607 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 372 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 21 glycan, 7 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q6NSJ0
- Elsewhere: RCSB PDB 7QQF · PDBe 7QQF · UniProt Q6NSJ0
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