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Structure of the xylo-oligosaccharide specific solute binding protein from bifidobacterium animalis subsp. lactis bl-04 in complex with xylotetraose

Analyse Structure of the xylo-oligosaccharide specific solute binding protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZKK
Type: protein
Length: 396 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xos binding protein
UniProt: C6A6Z1
Ligands: XYP
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xos binding protein	protein	396	49% helix, 16% strand	C6A6Z1

Ligands and binding sites

XYP · beta-D-xylopyranose · sugar · 4 copies · chains A
P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.80	0.86	55	XYP
2	190	0.46	0.74	28	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3ZKK · Structure of the xylo-oligosaccharide specific solute binding protein from… · 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 C6A6Z1
Elsewhere: RCSB PDB 3ZKK · PDBe 3ZKK · UniProt C6A6Z1

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