Research workbench
Crystal structure of er glucosidase II heterodimeric complex consisting of catalytic subunit and the binding domain of regulatory subunit
Analyse Crystal structure of er glucosidase II heterodimeric complex consisting of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JQP
- Type
- protein
- Length
- 1,049 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha glucosidase-like protein; Glucosidase 2 subunit beta-like protein
- UniProt
- G0SG42, G0S9M2
- Ligands
- CA
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha glucosidase-like protein | protein | 918 | 22% helix, 30% strand | G0SG42 |
| B | Glucosidase 2 subunit beta-like protein | protein | 131 | 14% helix, 11% strand | G0S9M2 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.67 | 0.86 | 45 | empty |
| 2 | 208 | 0.65 | 0.84 | 33 | empty |
| 3 | 306 | 0.62 | 0.79 | 49 | empty |
| 4 | 127 | 0.56 | 0.83 | 26 | TRS |
| 5 | 167 | 0.54 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1261 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5JQP · Crystal structure of ER glucosidase II heterodimeric complex consisting of catalytic… · the same entry in another collection · chain A against A, TM-score 1.00
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 G0SG42
- Every structure of UniProt G0S9M2
- Elsewhere: RCSB PDB 5JQP · PDBe 5JQP · UniProt G0SG42 · UniProt G0S9M2
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