Research workbench
Yeast glycogen synthase (GSY2P) basal state conformation
Analyse Yeast glycogen synthase (GSY2P) basal state conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NCH
- Type
- protein
- Length
- 2,448 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
- SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 611 | 49% helix, 15% strand | P27472 |
| B, D | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 612 | 49% helix, 15% strand | P27472 |
| C | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 613 | 51% helix, 15% strand | P27472 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 15 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.73 | 0.76 | 97 | SO4 |
| 2 | 931 | 0.73 | 0.77 | 84 | SO4 |
| 3 | 809 | 0.70 | 0.76 | 79 | SO4 |
| 4 | 754 | 0.70 | 0.76 | 68 | SO4 |
| 5 | 509 | 0.63 | 0.76 | 65 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1173 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 1166 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1015 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 949 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 181 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3NCH · Yeast Glycogen Synthase (Gsy2p) Basal State Conformation · 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 B 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 3NCH · PDBe 3NCH · UniProt P27472
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