Research workbench

Structural basis for the recruitment of glycogen synthase by glycogenin

Analyse Structural basis for the recruitment of glycogen synthase by glycogenin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QLB
Type: protein
Length: 2,725 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable glycogen [starch] synthase; Protein gyg-1, isoform B
EC: 2.4.1.11
UniProt: Q9U2D9, Q95Q50
Ligands: SO4
Pockets: 20 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable glycogen [starch] synthase (EC 2.4.1.11)	protein	650	50% helix, 14% strand	Q9U2D9
C	Probable glycogen [starch] synthase (EC 2.4.1.11)	protein	646	50% helix, 13% strand	Q9U2D9
D	Probable glycogen [starch] synthase (EC 2.4.1.11)	protein	651	49% helix, 13% strand	Q9U2D9
B	Probable glycogen [starch] synthase (EC 2.4.1.11)	protein	642	51% helix, 13% strand	Q9U2D9
G, E	Protein gyg-1, isoform B	protein	34	59% helix, 0% strand	Q95Q50
H	Protein gyg-1, isoform B	protein	33	61% helix, 0% strand	Q95Q50
F	Protein gyg-1, isoform B	protein	35	60% helix, 0% strand	Q95Q50

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains A, C, D, B
GOL · Glycerol · additive · 3 copies · chains C, D, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	751	0.70	0.77	71	empty
2	709	0.68	0.76	78	GOL
3	549	0.66	0.77	52	empty
4	501	0.66	0.77	50	empty
5	422	0.61	0.76	34	empty

Interfaces

10 interfaces between chains.

D–B · 1426 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 1425 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 1171 Å² buried · 8 hydrogen bonds · protein-protein
C–G · 1139 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 1100 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4QLB · Structural Basis for the Recruitment of Glycogen Synthase by Glycogenin · the same entry in another collection · chain F against F, TM-score 1.00
Q9U2D9 · AlphaFold monomer V2.0 prediction for glycogen [starch] synthase (Q9U2D9) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9U2D9
Every structure of UniProt Q95Q50
Elsewhere: RCSB PDB 4QLB · PDBe 4QLB · UniProt Q9U2D9 · UniProt Q95Q50

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.