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2'-fucosyllactose and 3-fucosyllactose binding protein from bifidobacterium longum infantis, bound with 2'-fucosyllactose
Analyse 2'-fucosyllactose and 3-fucosyllactose binding protein from bifidobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HUR
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter substrate-binding protein
- UniProt
- A0A1S2VYK0
- Ligands
- GLC, GAL, FUC, BGC, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ABC transporter substrate-binding protein | protein | 428 | 46% helix, 18% strand | A0A1S2VYK0 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 5 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.69 | 0.79 | 58 | GLC, GAL, FUC, PG0, BGC |
| 2 | 82 | 0.41 | 0.78 | 20 | empty |
| 3 | 66 | 0.33 | 0.76 | 13 | empty |
Compared structures
- 6HUR · 2'-fucosyllactose and 3-fucosyllactose binding protein from Bifidobacterium 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 A0A1S2VYK0
- Elsewhere: RCSB PDB 6HUR · PDBe 6HUR · UniProt A0A1S2VYK0
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