MolNFT v1 · #77912 · protein
Maltodextarn bound activated state form of yeast glycogen synthase isoform 2
3RT1 · Protein (glycogen [starch] synthase isoform 2): “Maltodextarn bound activated state form of yeast glycogen synthase isoform 2”. X-ray diffraction, 2 ligands (G6P, GLC), 20 pockets (best druggability 0.75). MolNFT v1 #77912 on…
- PDB
- 3RT1
- Type
- protein
- Length
- 2,558 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (glycogen [starch] synthase isoform 2)
- EC
- 2.4.1.11
- UniProt
- P27472
- Ligands
- G6P, GLC
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (glycogen [starch] synthase isoform 2) (EC 2.4.1.11) | protein | 638 | 50% helix, 13% strand | P27472 |
| C | Protein (glycogen [starch] synthase isoform 2) (EC 2.4.1.11) | protein | 646 | 50% helix, 14% strand | P27472 |
| D | Protein (glycogen [starch] synthase isoform 2) (EC 2.4.1.11) | protein | 636 | 46% helix, 14% strand | P27472 |
Ligands and binding sites
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · ion · 25 copies · chains A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, B, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.75 | 0.78 | 123 | G6P, PEG |
| 2 | 845 | 0.75 | 0.78 | 73 | G6P |
| 3 | 703 | 0.73 | 0.79 | 77 | PEG |
| 4 | 766 | 0.70 | 0.77 | 73 | empty |
| 5 | 645 | 0.70 | 0.78 | 62 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1652 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1651 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 779 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 757 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3RT1 · Maltodextarn bound activated state form of yeast glycogen synthase isoform 2 · 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 C 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 3RT1 · PDBe 3RT1 · UniProt P27472
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