Research workbench
Isoprimeverose-producing enzyme from aspergillus oryzae in complex with isoprimeverose
Analyse Isoprimeverose-producing enzyme from aspergillus oryzae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YOT
- Type
- protein
- Length
- 1,508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoprimeverose-producing enzyme
- UniProt
- Q2U8V9
- Ligands
- NAG, CA
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoprimeverose-producing enzyme | protein | 754 | 33% helix, 20% strand | Q2U8V9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.83 | 0.97 | 32 | GOL |
| 2 | 472 | 0.75 | 0.84 | 68 | GOL |
| 3 | 384 | 0.73 | 0.84 | 48 | empty |
| 4 | 487 | 0.67 | 0.78 | 58 | empty |
| 5 | 601 | 0.67 | 0.76 | 78 | empty |
Interfaces
1 interface between chains.
- A–B · 3019 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5YOT · Isoprimeverose-producing enzyme from Aspergillus oryzae in complex with isoprimeverose · 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 Q2U8V9
- Elsewhere: RCSB PDB 5YOT · PDBe 5YOT · UniProt Q2U8V9
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