Research workbench
Crystal structure of putative beta-galactosidase from bacteroides fragilis
Analyse Crystal structure of putative beta-galactosidase from bacteroides fragilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FN9
- Type
- protein
- Length
- 2,683 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- Q5LJ68
- Ligands
- CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative beta-galactosidase (EC 3.2.1.23) | protein | 672 | 17% helix, 38% strand | Q5LJ68 |
| C | Putative beta-galactosidase (EC 3.2.1.23) | protein | 673 | 17% helix, 39% strand | Q5LJ68 |
| D | Putative beta-galactosidase (EC 3.2.1.23) | protein | 666 | 17% helix, 38% strand | Q5LJ68 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.81 | 0.89 | 73 | empty |
| 2 | 335 | 0.80 | 0.90 | 53 | empty |
| 3 | 508 | 0.79 | 0.86 | 84 | empty |
| 4 | 419 | 0.79 | 0.88 | 62 | empty |
| 5 | 1191 | 0.74 | 0.77 | 108 | CL |
Interfaces
5 interfaces between chains.
- C–D · 2393 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2381 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 522 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 80 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3FN9 · Crystal structure of putative beta-galactosidase from bacteroides fragilis · 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 Q5LJ68
- Elsewhere: RCSB PDB 3FN9 · PDBe 3FN9 · UniProt Q5LJ68
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