MolNFT v1 · #140921 · protein
Isoprimeverose-producing enzyme from aspergillus oryzae in complex with isoprimeverose
5YQS: “Isoprimeverose-producing enzyme from aspergillus oryzae in complex with isoprimeverose”. X-ray diffraction, 5 ligands (NAG, XYS, BGC), 10 pockets (best druggability 0.82). MolNFT v1 #140921 on GenesisL1: 3D structure, binding sites…
- PDB
- 5YQS
- 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, XYS, BGC, GLC, CA
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoprimeverose-producing enzyme | protein | 754 | 32% helix, 20% strand | Q2U8V9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 5 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.82 | 0.96 | 32 | empty |
| 2 | 435 | 0.77 | 0.85 | 65 | empty |
| 3 | 456 | 0.74 | 0.83 | 67 | empty |
| 4 | 574 | 0.68 | 0.78 | 66 | empty |
| 5 | 522 | 0.63 | 0.76 | 64 | empty |
Interfaces
1 interface between chains.
- A–B · 3007 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 5YQS · 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 5YQS · PDBe 5YQS · UniProt Q2U8V9
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