Research workbench
Crystal structure of myorg bound to 1-deoxygalactonojirimycin
Analyse Crystal structure of myorg bound to 1-deoxygalactonojirimycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QQG
- Type
- protein
- Length
- 2,351 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
- DGJ, NAG, FUC
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 618 | 26% helix, 28% strand | Q6NSJ0 |
| B | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 623 | 26% helix, 29% strand | Q6NSJ0 |
| C | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 614 | 26% helix, 29% strand | Q6NSJ0 |
| D | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 496 | 31% helix, 19% strand | Q6NSJ0 |
Ligands and binding sites
- DGJ · (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · chains A
- MLI · Malonate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.71 | 0.91 | 19 | empty |
| 2 | 492 | 0.67 | 0.78 | 59 | empty |
| 3 | 494 | 0.67 | 0.78 | 62 | empty |
| 4 | 395 | 0.58 | 0.75 | 54 | empty |
| 5 | 205 | 0.57 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 668 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 642 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 275 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QQG · Crystal structure of MYORG bound to 1-deoxygalactonojirimycin · the same entry in another collection · chain D against D, TM-score 1.00
- Q6NSJ0 · AlphaFold monomer V2.0 prediction for myogenesis-regulating glycosidase (Q6NSJ0) · a predicted model of the same protein · chain D 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 Q6NSJ0
- Elsewhere: RCSB PDB 7QQG · PDBe 7QQG · UniProt Q6NSJ0
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