MolNFT v1 · #156513 · protein
The crystal structure of glycosidase hydrolyzing notoginsenoside
6M6L · Beta-glucosidase: “The crystal structure of glycosidase hydrolyzing notoginsenoside”. X-ray diffraction, 1 ligand (XYP), 6 pockets (best druggability 0.72). MolNFT v1 #156513 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6M6L
- Type
- protein
- Length
- 892 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- D2PL27
- Ligands
- XYP
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 447 | 43% helix, 16% strand | D2PL27 |
| B | Beta-glucosidase (EC 3.2.1.21) | protein | 445 | 43% helix, 16% strand | D2PL27 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.72 | 0.82 | 46 | XYP |
| 2 | 359 | 0.71 | 0.83 | 47 | empty |
| 3 | 245 | 0.62 | 0.81 | 46 | empty |
| 4 | 227 | 0.57 | 0.79 | 48 | empty |
| 5 | 100 | 0.52 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 602 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6M6L · The crystal structure of glycosidase hydrolyzing Notoginsenoside · 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 D2PL27
- Elsewhere: RCSB PDB 6M6L · PDBe 6M6L · UniProt D2PL27
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