MolNFT v1 · #84398 · protein
Crystal structure of ttb-gly F401S mutant
3ZJK · Beta glycosidase: “Crystal structure of ttb-gly F401S mutant”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.73). MolNFT v1 #84398 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZJK
- Type
- protein
- Length
- 1,272 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta glycosidase
- EC
- 3.2.1.21
- UniProt
- Q9RA61
- Ligands
- CL
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta glycosidase (EC 3.2.1.21) | protein | 424 | 40% helix, 18% strand | Q9RA61 |
| B | Beta glycosidase (EC 3.2.1.21) | protein | 423 | 40% helix, 19% strand | Q9RA61 |
| C | Beta glycosidase (EC 3.2.1.21) | protein | 425 | 40% helix, 18% strand | Q9RA61 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.73 | 0.83 | 42 | GOL |
| 2 | 440 | 0.72 | 0.82 | 46 | GOL |
| 3 | 422 | 0.71 | 0.82 | 46 | GOL |
| 4 | 90 | 0.64 | 0.90 | 17 | empty |
| 5 | 234 | 0.63 | 0.82 | 47 | empty |
Interfaces
2 interfaces between chains.
- A–B · 878 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 669 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3ZJK · crystal structure of Ttb-gly F401S mutant · 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 Q9RA61
- Elsewhere: RCSB PDB 3ZJK · PDBe 3ZJK · UniProt Q9RA61
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