Research workbench
Crystal structure of myorg (D520N) in complex with gal-A1,4-glc
Analyse Crystal structure of myorg (D520N) in complex with gal-A1,4-glc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QQH
- Type
- protein
- Length
- 2,468 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, BGC, GLA
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 615 | 27% helix, 29% strand | Q6NSJ0 |
| B, D | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 618 | 26% helix, 29% strand | Q6NSJ0 |
| C | Myogenesis-regulating glycosidase (EC 3.2.1.-) | protein | 617 | 26% helix, 29% strand | Q6NSJ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.66 | 0.77 | 60 | empty |
| 2 | 88 | 0.65 | 0.90 | 19 | EDO |
| 3 | 291 | 0.61 | 0.79 | 44 | empty |
| 4 | 505 | 0.60 | 0.74 | 61 | empty |
| 5 | 181 | 0.48 | 0.76 | 37 | empty |
Interfaces
3 interfaces between chains.
- B–C · 718 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 681 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 7QQH · Crystal structure of MYORG (D520N) in complex with Gal-a1,4-Glc · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NSJ0 · AlphaFold monomer V2.0 prediction for myogenesis-regulating glycosidase (Q6NSJ0) · a predicted model of the same protein · chain A 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 7QQH · PDBe 7QQH · UniProt Q6NSJ0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.