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Crystal structure of gpb in complex with DK10

Analyse Crystal structure of gpb in complex with DK10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4EJ2
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: D1F
Pockets: 12 · best druggability 0.83

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

D1F · 1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione · 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	317	0.83	0.94	41	D1F
2	85	0.73	0.96	28	empty
3	50	0.70	0.98	17	empty
4	301	0.68	0.83	39	empty
5	110	0.51	0.81	22	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

4EJ2 · Crystal structure of GPb in complex with DK10 · 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 4EJ2 · PDBe 4EJ2 · UniProt P00489

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