MolNFT v1 · #136536 · protein
Activated yeast glycogen synthase in complex with udp glucosamine
5UW4 · Glycogen [starch] synthase isoform 2: “Activated yeast glycogen synthase in complex with udp glucosamine”. X-ray diffraction, 3 ligands (UDP, G6P, GCS), 20 pockets (best druggability 0.80). MolNFT v1 #136536 on GenesisL1: 3D…
- PDB
- 5UW4
- Type
- protein
- Length
- 2,548 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
- UDP, G6P, GCS
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 638 | 49% helix, 14% strand | P27472 |
| B, D | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 636 | 48% helix, 14% strand | P27472 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains C, B, A, D
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains C, B, A, D
- GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.80 | 0.82 | 98 | GCS, UDP |
| 2 | 1135 | 0.74 | 0.77 | 125 | G6P |
| 3 | 738 | 0.73 | 0.79 | 73 | empty |
| 4 | 834 | 0.70 | 0.76 | 86 | UDP |
| 5 | 682 | 0.68 | 0.76 | 60 | UDP |
Interfaces
6 interfaces between chains.
- C–D · 1653 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 1651 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 756 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 726 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5UW4 · Activated yeast Glycogen Synthase in complex with UDP glucosamine · the same entry in another collection · chain C against C, 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 B 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 P27472
- Elsewhere: RCSB PDB 5UW4 · PDBe 5UW4 · UniProt P27472
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