Research workbench
Glycogen synthase in complex with udp and glucosamine
Analyse Glycogen synthase in complex with udp and glucosamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VNC
- 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 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 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 | 636 | 48% helix, 15% strand | P27472 |
| D | Glycogen [starch] synthase isoform 2 (EC 2.4.1.11) | protein | 636 | 47% helix, 14% strand | P27472 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains A, D, B, C
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.77 | 0.79 | 109 | GCS, UDP |
| 2 | 532 | 0.72 | 0.81 | 58 | empty |
| 3 | 849 | 0.71 | 0.76 | 90 | UDP |
| 4 | 500 | 0.70 | 0.80 | 53 | empty |
| 5 | 697 | 0.69 | 0.77 | 63 | UDP |
Interfaces
6 interfaces between chains.
- C–D · 1639 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 751 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 731 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 499 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5VNC · Glycogen synthase in complex with UDP and glucosamine · the same entry in another collection · chain A against A, 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 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 P27472
- Elsewhere: RCSB PDB 5VNC · PDBe 5VNC · UniProt P27472
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