Research workbench
Native structure of beta-galactosidase from penicillium sp. in complex with galactose
Analyse Native structure of beta-galactosidase from penicillium sp. in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XC6
- Type
- protein
- Length
- 971 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- Ligands
- NAG, MAN, BMA, GAL, NA, IOD, PO4
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 971 | 16% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- NA · Sodium ion · metal · chains A
- IOD · Iodide ion · ion · 52 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.73 | 0.98 | 35 | EDO |
| 2 | 52 | 0.59 | 0.91 | 19 | EDO |
| 3 | 134 | 0.55 | 0.82 | 30 | empty |
| 4 | 115 | 0.45 | 0.78 | 28 | GAL, IOD |
| 5 | 115 | 0.41 | 0.76 | 19 | NAG, IOD |
Modifications
Observed in the structure: 7 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 1XC6 · Native Structure Of Beta-Galactosidase from Penicillium sp. in complex with Galactose · 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
- Elsewhere: RCSB PDB 1XC6 · PDBe 1XC6
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