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Glycogen phosphorylase complexed with 2,5-dihydroxy-4-(beta-D- glucopyranosyl)-bromo-benzene

Analyse Glycogen phosphorylase complexed with 2,5-dihydroxy-4-(beta-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NPA
Type: protein
Length: 810 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: Z57
Pockets: 11 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycogen phosphorylase, muscle form (EC 2.4.1.1)	protein	810	52% helix, 15% strand	P00489

Ligands and binding sites

Z57 · (1S)-1,5-anhydro-1-(4-bromo-2,5-dihydroxyphenyl)-D-glucitol · ligand · chains A

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

Pockets

11 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	157	0.80	0.96	32	Z57
2	137	0.79	0.96	41	empty
3	442	0.69	0.80	55	empty
4	221	0.55	0.78	27	empty
5	103	0.53	0.83	21	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

3NPA · Glycogen phosphorylase complexed with 2,5-dihydroxy-4-(beta-D-glucopyranosyl)-bromo-benzen… · 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 3NPA · PDBe 3NPA · UniProt P00489

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