Research workbench
Crystal structure of pyrococcus abyssi glycogen synthase with open and closed conformations
Analyse Crystal structure of pyrococcus abyssi glycogen synthase with open and closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FRO
- Type
- protein
- Length
- 1,317 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
- NHF, PO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glga glycogen synthase (EC 2.4.1.21) | protein | 439 | 43% helix, 21% strand | Q9V2J8 |
Ligands and binding sites
- NHF · 1,5-anhydro-D-fructose · ligand · chains B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.81 | 0.85 | 55 | NHF |
| 2 | 924 | 0.75 | 0.78 | 67 | empty |
| 3 | 790 | 0.71 | 0.77 | 61 | empty |
| 4 | 156 | 0.48 | 0.77 | 21 | PO4 |
| 5 | 146 | 0.45 | 0.76 | 20 | PO4 |
Interfaces
3 interfaces between chains.
- B–C · 739 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 726 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 715 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3FRO · Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed… · 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 3FRO · PDBe 3FRO · UniProt Q9V2J8
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