MolNFT v1 · #134112 · protein
G6P bound activated state of yeast glycogen synthase 2
5SUK · Glycogen [starch] synthase isoform 2: “G6P bound activated state of yeast glycogen synthase 2”. X-ray diffraction, 1 ligand (G6P), 20 pockets (best druggability 0.75). MolNFT v1 #134112 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5SUK
- Type
- protein
- Length
- 2,518 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 0.75
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 638 | 50% helix, 14% strand | P27472 |
| B | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 637 | 49% helix, 15% strand | P27472 |
| C | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 639 | 49% helix, 14% strand | P27472 |
| D | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 604 | 50% helix, 14% strand | P27472 |
Ligands and binding sites
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 6 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.75 | 0.78 | 73 | G6P |
| 2 | 900 | 0.73 | 0.77 | 86 | empty |
| 3 | 53 | 0.71 | 0.98 | 16 | empty |
| 4 | 685 | 0.70 | 0.77 | 58 | empty |
| 5 | 658 | 0.69 | 0.77 | 94 | G6P |
Interfaces
6 interfaces between chains.
- A–C · 1648 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1645 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 783 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 736 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 498 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5SUK · G6P bound activated state of yeast glycogen synthase 2 · 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 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 P27472
- Elsewhere: RCSB PDB 5SUK · PDBe 5SUK · UniProt P27472
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