MolNFT v1 · #104791 · protein
Structural basis for the recruitment of glycogen synthase by glycogenin
4QLB · Probable glycogen [starch] synthase: “Structural basis for the recruitment of glycogen synthase by glycogenin”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.70). MolNFT v1 #104791 on GenesisL1: 3D structure…
- PDB
- 4QLB
- Type
- protein
- Length
- 2,725 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable glycogen [starch] synthase; Protein gyg-1, isoform B
- EC
- 2.4.1.11
- UniProt
- Q9U2D9, Q95Q50
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable glycogen [starch] synthase (EC 2.4.1.11) | protein | 650 | 50% helix, 14% strand | Q9U2D9 |
| C | Probable glycogen [starch] synthase (EC 2.4.1.11) | protein | 646 | 50% helix, 13% strand | Q9U2D9 |
| D | Probable glycogen [starch] synthase (EC 2.4.1.11) | protein | 651 | 49% helix, 13% strand | Q9U2D9 |
| B | Probable glycogen [starch] synthase (EC 2.4.1.11) | protein | 642 | 51% helix, 13% strand | Q9U2D9 |
| G, E | Protein gyg-1, isoform B | protein | 34 | 59% helix, 0% strand | Q95Q50 |
| H | Protein gyg-1, isoform B | protein | 33 | 61% helix, 0% strand | Q95Q50 |
| F | Protein gyg-1, isoform B | protein | 35 | 60% helix, 0% strand | Q95Q50 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, C, D, B
- GOL · Glycerol · additive · 3 copies · chains C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.70 | 0.77 | 71 | empty |
| 2 | 709 | 0.68 | 0.76 | 78 | GOL |
| 3 | 549 | 0.66 | 0.77 | 52 | empty |
| 4 | 501 | 0.66 | 0.77 | 50 | empty |
| 5 | 422 | 0.61 | 0.76 | 34 | empty |
Interfaces
10 interfaces between chains.
- D–B · 1426 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 1425 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 1171 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 1139 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 1100 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4QLB · Structural Basis for the Recruitment of Glycogen Synthase by Glycogenin · the same entry in another collection · chain F against F, TM-score 1.00
- Q9U2D9 · AlphaFold monomer V2.0 prediction for glycogen [starch] synthase (Q9U2D9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9U2D9
- Every structure of UniProt Q95Q50
- Elsewhere: RCSB PDB 4QLB · PDBe 4QLB · UniProt Q9U2D9 · UniProt Q95Q50
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