Research workbench
GLUCOSE1,2CYCLIC phosphate bound activated state of yeast glycogen synthase
Analyse GLUCOSE1,2CYCLIC phosphate bound activated state 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
- 4KQ2
- Type
- protein
- Length
- 2,550 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GSY2P
- UniProt
- E7NKU1
- Ligands
- U5P, 1S3, G6P, BA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | GSY2P | protein | 638 | 48% helix, 14% strand | E7NKU1 |
| D | GSY2P | protein | 636 | 48% helix, 14% strand | E7NKU1 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- 1S3 · (2R,3aR,5R,6S,7S,7aR)-5-(hydroxymethyl)tetrahydro-3aH-[1,3,2]dioxaphospholo[4,5-b]pyran-2,6,7-triol 2-oxide · ligand · chains C
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains A, D, B, C
- BA · Barium ion · metal · 7 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.76 | 0.79 | 76 | 1S3, U5P |
| 2 | 833 | 0.73 | 0.78 | 77 | U5P |
| 3 | 700 | 0.72 | 0.78 | 57 | U5P |
| 4 | 712 | 0.70 | 0.77 | 80 | U5P |
| 5 | 536 | 0.70 | 0.80 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1667 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1657 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 780 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 771 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 505 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4KQ2 · Glucose1,2cyclic phosphate bound activated state of Yeast Glycogen Synthase · 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 E7NKU1
- Elsewhere: RCSB PDB 4KQ2 · PDBe 4KQ2 · UniProt E7NKU1
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