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Glycogen phosphorylase B in complex with beta-D-glucopyranonucleoside 5-fluorouracil

Analyse Glycogen phosphorylase B in complex with beta-D-glucopyranonucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SYR
Type: protein
Length: 807 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycogen phosphorylase, muscle form
EC: 2.4.1.1
UniProt: P00489
Ligands: GPK
Pockets: 13 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycogen phosphorylase, muscle form (EC 2.4.1.1)	protein	807	53% helix, 16% strand	P00489

Ligands and binding sites

GPK · 5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione · ligand · chains A

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	147	0.79	0.96	32	GPK
2	88	0.73	0.95	28	empty
3	271	0.70	0.85	32	empty
4	50	0.69	0.98	18	empty
5	110	0.51	0.82	21	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

3SYR · Glycogen phosphorylase b in complex with beta-D-glucopyranonucleoside 5-fluorouracil · 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 3SYR · PDBe 3SYR · UniProt P00489

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