Research workbench
Maltodextran bound basal state conformation of yeast glycogen synthase isoform 2
Analyse Maltodextran bound basal state conformation of yeast glycogen synthase isoform 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RSZ
- Type
- protein
- Length
- 2,455 residues
- Chains
- 6
- 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
- GLC, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 611 | 50% helix, 15% strand | P27472 |
| C, D | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 613 | 51% helix, 15% strand | P27472 |
| E | Glycogen [starch] synthase isoform 2 | protein | 2 | 0% helix, 0% strand | — |
| F | Glycogen [starch] synthase isoform 2 | protein | 5 | 60% helix, 0% strand | — |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A, B
- SO4 · Sulfate ion · ion · 16 copies · chains A, D, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.74 | 0.77 | 101 | SO4 |
| 2 | 1045 | 0.73 | 0.76 | 82 | SO4 |
| 3 | 800 | 0.73 | 0.78 | 71 | SO4 |
| 4 | 958 | 0.72 | 0.76 | 82 | SO4 |
| 5 | 467 | 0.61 | 0.76 | 50 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1189 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 1188 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 958 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 886 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 283 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3RSZ · Maltodextran bound basal state conformation of yeast glycogen synthase isoform 2 · the same entry in another collection · chain B against B, 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 0.99
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 3RSZ · PDBe 3RSZ · UniProt P27472
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