Research workbench
Human GYS1-GYG1 complex activated state bound to glucose-6-phosphate, uridine diphosphate, and glucose
Analyse Human GYS1-GYG1 complex activated state bound to glucose-6-phosphate, uridine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q13
- Type
- protein
- Length
- 2,488 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen [starch] synthase, muscle; Glycogenin-1
- EC
- 2.4.1.11, 2.4.1.186
- UniProt
- P13807, P46976
- Ligands
- UDP, G6P, GLC
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glycogen [starch] synthase, muscle (EC 2.4.1.11) | protein | 590 | 44% helix, 12% strand | P13807 |
| E, F, G, H | Glycogenin-1 (EC 2.4.1.186) | protein | 32 | 63% helix, 0% strand | P46976 |
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, C, B, D
- GLC · alpha-D-glucopyranose · sugar · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.80 | 0.81 | 96 | UDP, GLC |
| 2 | 954 | 0.79 | 0.81 | 96 | UDP, GLC |
| 3 | 963 | 0.79 | 0.81 | 96 | UDP, GLC |
| 4 | 932 | 0.79 | 0.81 | 91 | UDP, GLC |
| 5 | 343 | 0.65 | 0.80 | 53 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1512 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 1508 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1290 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 1279 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 1094 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7Q13 · Human GYS1-GYG1 complex activated state bound to glucose-6-phosphate, uridine… · the same entry in another collection · chain D against D, TM-score 1.00
- P13807 · AlphaFold monomer V2.0 prediction for glycogen [starch] synthase, muscle (P13807) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P13807
- Every structure of UniProt P46976
- Elsewhere: RCSB PDB 7Q13 · PDBe 7Q13 · UniProt P13807 · UniProt P46976
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