MolNFT v1 · #129360 · protein
A GH31 family sulfoquinovosidase in complex with aza-sugar inhibitor ifgsq
5OHY · Alpha-glucosidase yihq: “A GH31 family sulfoquinovosidase in complex with aza-sugar inhibitor ifgsq”. X-ray diffraction, 4 ligands (9VH, K, SCN), 20 pockets (best druggability 0.79). MolNFT v1 #129360 on GenesisL1: 3D structure…
- PDB
- 5OHY
- Type
- protein
- Length
- 2,637 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase yihq
- EC
- 3.2.1.20
- UniProt
- A0A083ZKV2
- Ligands
- 9VH, K, SCN, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 660 | 27% helix, 29% strand | A0A083ZKV2 |
| B | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 663 | 27% helix, 30% strand | A0A083ZKV2 |
| C | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 660 | 27% helix, 29% strand | A0A083ZKV2 |
| D | Alpha-glucosidase yihq (EC 3.2.1.20) | protein | 654 | 27% helix, 30% strand | A0A083ZKV2 |
Ligands and binding sites
- 9VH · [(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methanesulfonic acid · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.79 | 0.87 | 37 | EDO, 9VH |
| 2 | 287 | 0.78 | 0.90 | 38 | EDO, 9VH |
| 3 | 296 | 0.77 | 0.89 | 41 | EDO, 9VH |
| 4 | 301 | 0.76 | 0.88 | 38 | EDO, 9VH |
| 5 | 578 | 0.69 | 0.78 | 61 | SCN |
Interfaces
5 interfaces between chains.
- B–C · 504 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 353 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5OHY · A GH31 family sulfoquinovosidase in complex with aza-sugar inhibitor IFGSQ · 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 A0A083ZKV2
- Elsewhere: RCSB PDB 5OHY · PDBe 5OHY · UniProt A0A083ZKV2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.