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Glycogen phosphorylase in complex with gallic acid

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

PDB: 4Z5X
Type: protein
Length: 811 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: GDE, PLP
Pockets: 13 · best druggability 0.85

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	811	53% helix, 15% strand	P00489

Ligands and binding sites

GDE · 3,4,5-trihydroxybenzoic acid · ligand · chains A
PLP · Pyridoxal-5'-phosphate · 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	301	0.85	0.96	49	PLP
2	139	0.79	0.96	39	empty
3	428	0.71	0.82	51	empty
4	132	0.53	0.81	20	empty
5	110	0.51	0.81	24	empty

Modifications

Observed in the structure: 1 cofactor, 1 modified (pyridoxal phosphate Schiff base, oxidation).

Compared structures

4Z5X · Glycogen phosphorylase in complex with gallic 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 4Z5X · PDBe 4Z5X · UniProt P00489

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