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Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure

Analyse Effects of commonly used cryoprotectants on glycogen phosphorylase activity and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BX3
Type: protein
Length: 801 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (glycogen phosphorylase B)
EC: 2.4.1.1
UniProt: P00489
Ligands: PLP
Pockets: 12 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein (glycogen phosphorylase B) (EC 2.4.1.1)	protein	801	54% helix, 15% strand	P00489

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · chains A

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	298	0.84	0.95	52	PLP
2	70	0.71	0.96	25	empty
3	219	0.69	0.86	31	empty
4	114	0.54	0.83	19	empty
5	225	0.50	0.75	29	empty

Modifications

Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1BX3 · Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure · 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 P00489
Elsewhere: RCSB PDB 1BX3 · PDBe 1BX3 · UniProt P00489

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