MolNFT v1 · #73483 · protein

Glycogen synthase basal state udp complex

3O3C · Glycogen [starch] synthase isoform 2: “Glycogen synthase basal state udp complex”. X-ray diffraction, 2 ligands (UDP, SO4), 20 pockets (best druggability 0.72). MolNFT v1 #73483 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3O3C
Type: protein
Length: 2,444 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycogen [starch] synthase isoform 2
EC: 2.4.1.11
UniProt: P27472
Ligands: UDP, SO4
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glycogen [starch] synthase isoform 2 (EC 2.4.1.11)	protein	611	51% helix, 15% strand	P27472

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D

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

Pockets

20 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	907	0.72	0.76	75	SO4, UDP
2	864	0.72	0.77	80	SO4, UDP
3	953	0.71	0.76	94	SO4, UDP
4	866	0.71	0.76	72	SO4, UDP
5	459	0.61	0.75	46	empty

Interfaces

6 interfaces between chains.

A–C · 1179 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 1135 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 974 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 907 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 27 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3O3C · Glycogen synthase basal state UDP complex · the same entry in another collection · chain A against A, TM-score 1.00
P27472 · AlphaFold monomer V2.0 prediction for glycogen [starch] synthase isoform 2 (P27472) · 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 P27472
Elsewhere: RCSB PDB 3O3C · PDBe 3O3C · UniProt P27472

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