MolNFT v1 · #58758 · protein

Glycogen phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid

3BD6 · Glycogen phosphorylase, muscle form: “Glycogen phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid”. X-ray diffraction, 1 ligand (RDD), 13 pockets (best druggability 0.79). MolNFT v1 #58758 on GenesisL1: 3D structure…

PDB: 3BD6
Type: protein
Length: 813 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: RDD
Pockets: 13 · best druggability 0.79

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	813	52% helix, 15% strand	P00489

Ligands and binding sites

RDD · 1-beta-D-ribofuranosyl-1,3,5-triazinane-2,4,6-trione · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.79	0.97	36	empty
2	86	0.73	0.96	26	empty
3	306	0.68	0.83	43	empty
4	197	0.52	0.77	19	RDD
5	106	0.51	0.81	17	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

3BD6 · Glycogen Phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid · 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 3BD6 · PDBe 3BD6 · UniProt P00489

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