MolNFT v1 · #191249 · protein
Human glycogenin-1 and glycogen synthase-1 complex in the presence of glucose-6-phosphate
8CVX · Glycogen [starch] synthase, muscle: “Human glycogenin-1 and glycogen synthase-1 complex in the presence of glucose-6-phosphate”. Electron microscopy, 1 ligand (G6P), 20 pockets (best druggability 0.65). MolNFT v1 #191249 on…
- PDB
- 8CVX
- Type
- protein
- Length
- 2,541 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
- G6P
- Pockets
- 20 · best druggability 0.65
Structure
electron microscopy · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen [starch] synthase, muscle (EC 2.4.1.11) | protein | 602 | 46% helix, 14% strand | P13807 |
| E, H | Glycogenin-1 (EC 2.4.1.186) | protein | 33 | 58% helix, 0% strand | P46976 |
| G, F | Glycogenin-1 (EC 2.4.1.186) | protein | 32 | 59% helix, 0% strand | P46976 |
| B, D, C | Glycogen [starch] synthase, muscle (EC 2.4.1.11) | protein | 603 | 45% helix, 13% strand | P13807 |
Ligands and binding sites
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 4 copies · chains A, C, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.65 | 0.77 | 52 | empty |
| 2 | 570 | 0.63 | 0.75 | 61 | empty |
| 3 | 504 | 0.62 | 0.75 | 48 | empty |
| 4 | 360 | 0.62 | 0.78 | 40 | empty |
| 5 | 393 | 0.62 | 0.77 | 45 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1667 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1641 Ų buried · 7 hydrogen bonds · protein-protein
- H–D · 1193 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1154 Ų buried · 9 hydrogen bonds · protein-protein
- F–B · 1144 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 8CVX · Human glycogenin-1 and glycogen synthase-1 complex in the presence of glucose-6-phosphate · the same entry in another collection · chain C against C, TM-score 1.00
- P13807 · AlphaFold monomer V2.0 prediction for glycogen [starch] synthase, muscle (P13807) · 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 P13807
- Every structure of UniProt P46976
- Elsewhere: RCSB PDB 8CVX · PDBe 8CVX · UniProt P13807 · UniProt P46976
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