MolNFT v1 · #99921 · protein

Crystal structure of gpb in complex with sugar (N-[4-(5,6,7,8- tetrahydronaphthalen-2-YL)BUTANOYL]-beta-D-glucopyranosylamine)

4MI6 · Glycogen phosphorylase, muscle form: “Crystal structure of gpb in complex with sugar (N-[4-(5,6,7,8…”. X-ray diffraction, 1 ligand (26V), 12 pockets (best druggability 0.83). MolNFT v1 #99921 on GenesisL1: 3D structure, binding…

PDB: 4MI6
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: 26V
Pockets: 12 · best druggability 0.83

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	810	53% helix, 15% strand	P00489

Ligands and binding sites

26V · N-[4-(5,6,7,8-tetrahydronaphthalen-2-yl)butanoyl]-beta-D-glucopyranosylamine · 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	253	0.83	0.95	43	26V
2	139	0.79	0.96	39	empty
3	281	0.67	0.83	37	empty
4	105	0.53	0.83	20	empty
5	115	0.52	0.82	19	empty

Modifications

Observed in the structure: 1 modified (cofactor).

Compared structures

4MI6 · Crystal structure of Gpb in complex with SUGAR… · 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 4MI6 · PDBe 4MI6 · UniProt P00489

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