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Crystal structure of glycogen phosphorylase DK5 complex

Analyse Crystal structure of glycogen phosphorylase DK5 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L7D
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: DK5
Pockets: 12 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycogen phosphorylase, muscle form (EC 2.4.1.1)	protein	809	53% helix, 15% strand	P00489

Ligands and binding sites

DK5 · 1-(2,3-dideoxy-3-fluoro-beta-D-arabino-hexopyranosyl)-4-[(phenylcarbonyl)amino]pyrimidin-2(1H)-one · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	236	0.82	0.95	42	DK5
2	139	0.79	0.97	40	empty
3	448	0.70	0.81	58	empty
4	112	0.52	0.82	19	empty
5	201	0.51	0.77	20	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

3L7D · Crystal Structure of Glycogen Phosphorylase DK5 complex · 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 3L7D · PDBe 3L7D · UniProt P00489

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