Research workbench
Glucose-6-phosphate activated form of yeast glycogen synthase
Analyse Glucose-6-phosphate activated form of yeast glycogen synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NB0
- Type
- protein
- Length
- 2,565 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
- G6P
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 638 | 51% helix, 15% strand | P27472 |
| B | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 645 | 50% helix, 14% strand | P27472 |
| C | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 646 | 51% helix, 15% strand | P27472 |
| D | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 636 | 50% helix, 14% strand | P27472 |
Ligands and binding sites
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 6 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.73 | 0.78 | 59 | G6P |
| 2 | 804 | 0.72 | 0.78 | 88 | PEG, G6P |
| 3 | 764 | 0.70 | 0.77 | 77 | empty |
| 4 | 730 | 0.70 | 0.77 | 84 | PEG |
| 5 | 708 | 0.69 | 0.77 | 67 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1650 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1641 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 802 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 777 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 536 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3NB0 · Glucose-6-Phosphate activated form of Yeast Glycogen Synthase · the same entry in another collection · chain D against D, 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 3NB0 · PDBe 3NB0 · UniProt P27472
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