MolNFT v1 · #170369 · protein

The crystal structure of glycogen phosphorylase in complex with 52

6Y5C · Glycogen phosphorylase, muscle form: “The crystal structure of glycogen phosphorylase in complex with 52”. X-ray diffraction, 1 ligand (O9T), 15 pockets (best druggability 0.80). MolNFT v1 #170369 on GenesisL1: 3D structure, binding…

PDB: 6Y5C
Type: protein
Length: 809 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: O9T
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycogen phosphorylase, muscle form (EC 2.4.1.1)	protein	809	52% helix, 16% strand	P00489

Ligands and binding sites

O9T · 2-(4-methylphenyl)-5,7-bis(oxidanyl)chromen-4-one · ligand · chains A

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

Pockets

15 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	0.80	0.97	40	empty
2	73	0.71	0.96	26	empty
3	271	0.68	0.83	35	empty
4	221	0.52	0.76	26	empty
5	114	0.51	0.81	20	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

6Y5C · The crystal structure of glycogen phosphorylase in complex with 52 · 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 6Y5C · PDBe 6Y5C · UniProt P00489

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