Research workbench
Crystal structure of beta-galactosidase from bacteroides cellulosilyticus
Analyse Crystal structure of beta-galactosidase from bacteroides cellulosilyticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SF2
- Type
- protein
- Length
- 3,515 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 2, sugar binding domain protein
- UniProt
- E2NBY7
- Ligands
- MG, CL, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F | Glycosyl hydrolase family 2, sugar binding domain protein | protein | 586 | 17% helix, 35% strand | E2NBY7 |
| C | Glycosyl hydrolase family 2, sugar binding domain protein | protein | 585 | 16% helix, 35% strand | E2NBY7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 14 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 9 copies · chains B, C, E, D, F
- EDO · 1,2-ethanediol · additive · 58 copies · chains A, B, C, D, F, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, B, C, D, E, F
- BME · Beta-mercaptoethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.76 | 0.84 | 60 | EDO |
| 2 | 461 | 0.76 | 0.85 | 56 | EDO |
| 3 | 527 | 0.75 | 0.83 | 79 | CL |
| 4 | 499 | 0.75 | 0.84 | 64 | empty |
| 5 | 467 | 0.75 | 0.84 | 61 | empty |
Interfaces
12 interfaces between chains.
- A–D · 703 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 691 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 684 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 611 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 589 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 7SF2 · Crystal Structure of Beta-Galactosidase from Bacteroides cellulosilyticus · 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 E2NBY7
- Elsewhere: RCSB PDB 7SF2 · PDBe 7SF2 · UniProt E2NBY7
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