Research workbench
Structure of glycogen synthase from pyrococcus abyssi
Analyse Structure of glycogen synthase from pyrococcus abyssi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BIS
- Type
- protein
- Length
- 1,320 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glga glycogen synthase
- EC
- 2.4.1.21
- UniProt
- Q9V2J8
- Ligands
- UDP, GLC
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glga glycogen synthase (EC 2.4.1.21) | protein | 440 | 42% helix, 20% strand | Q9V2J8 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains C
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, C
- DIO · 1,4-diethylene dioxide · additive · 10 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.73 | 0.77 | 58 | GOL |
| 2 | 813 | 0.73 | 0.77 | 64 | GOL |
| 3 | 703 | 0.68 | 0.76 | 64 | GOL |
| 4 | 214 | 0.58 | 0.80 | 20 | DIO |
| 5 | 175 | 0.50 | 0.77 | 22 | DIO |
Interfaces
3 interfaces between chains.
- A–B · 716 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 716 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 679 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 2BIS · Structure of glycogen synthase from Pyrococcus abyssi · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9V2J8
- Elsewhere: RCSB PDB 2BIS · PDBe 2BIS · UniProt Q9V2J8
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