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Structure of sucrose phosphorylase from bifidobacterium adolescentis bound to glycosylated resveratrol

Analyse Structure of sucrose phosphorylase from bifidobacterium adolescentis bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M9X
Type: protein
Length: 504 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sucrose phosphorylase
EC: 2.4.1.7
UniProt: Q84HQ2
Ligands: 7KP
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Sucrose phosphorylase (EC 2.4.1.7)	protein	504	38% helix, 20% strand	Q84HQ2

Ligands and binding sites

7KP · (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(~{E})-2-(4-hydroxyphenyl)ethenyl]-5-oxidanyl-phenoxy]oxane-3,4,5-triol · ligand · chains B

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	486	0.73	0.82	60	7KP
2	53	0.38	0.81	20	empty

Compared structures

5M9X · Structure of sucrose phosphorylase from Bifidobacterium adolescentis bound to… · the same entry in another collection · chain B against B, 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 Q84HQ2
Elsewhere: RCSB PDB 5M9X · PDBe 5M9X · UniProt Q84HQ2

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