MolNFT v1 · #90491 · protein

Crystal structure of gpb in complex with DK15

4EKY · Glycogen phosphorylase, muscle form: “Crystal structure of gpb in complex with DK15”. X-ray diffraction, 1 ligand (D1J), 13 pockets (best druggability 0.80). MolNFT v1 #90491 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4EKY
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: D1J
Pockets: 13 · 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	810	52% helix, 16% strand	P00489

Ligands and binding sites

D1J · 1-(beta-D-glucopyranosyl)-5-(pent-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

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	172	0.80	0.96	38	D1J
2	81	0.71	0.95	25	empty
3	326	0.67	0.82	40	empty
4	122	0.52	0.81	20	empty
5	223	0.51	0.76	21	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

4EKY · Crystal structure of GPb in complex with DK15 · 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 4EKY · PDBe 4EKY · UniProt P00489

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