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Crystal structure of lacto-N-biosidase lnbx from bifidobacterium longum subsp. longum, galacto-N-biose complex
Analyse Crystal structure of lacto-N-biosidase lnbx from bifidobacterium longum subsp.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GQG
- Type
- protein
- Length
- 1,164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lacto-N-biosidase
- EC
- 3.2.1.140
- UniProt
- A0A024QYS6
- Ligands
- NGA, GAL, CA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lacto-N-biosidase (EC 3.2.1.140) | protein | 582 | 7% helix, 35% strand | A0A024QYS6 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.69 | 0.80 | 62 | empty |
| 2 | 318 | 0.54 | 0.75 | 48 | NGA, GAL |
| 3 | 145 | 0.47 | 0.77 | 30 | NGA, GAL |
Interfaces
1 interface between chains.
- A–B · 731 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5GQG · Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum… · 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 A0A024QYS6
- Elsewhere: RCSB PDB 5GQG · PDBe 5GQG · UniProt A0A024QYS6
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