MolNFT v1 · #21108 · protein
Crystal structure of the glycogen synthase from a. tumefaciens in complex with ADP
1RZU · Glycogen synthase 1: “Crystal structure of the glycogen synthase from a. tumefaciens in complex with ADP”. X-ray diffraction, 1 ligand (ADP), 7 pockets (best druggability 0.77). MolNFT v1 #21108 on GenesisL1: 3D structure, binding…
- PDB
- 1RZU
- Type
- protein
- Length
- 955 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen synthase 1
- EC
- 2.4.1.21
- UniProt
- P0A3F3
- Ligands
- ADP
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen synthase 1 (EC 2.4.1.21) | protein | 477 | 40% helix, 20% strand | P0A3F3 |
| B | Glycogen synthase 1 (EC 2.4.1.21) | protein | 478 | 40% helix, 20% strand | P0A3F3 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.77 | 0.85 | 65 | empty |
| 2 | 534 | 0.76 | 0.83 | 52 | empty |
| 3 | 785 | 0.72 | 0.77 | 72 | ADP |
| 4 | 827 | 0.70 | 0.75 | 85 | ADP |
| 5 | 99 | 0.55 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 987 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1RZU · Crystal structure of the glycogen synthase from A. tumefaciens in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3F3 · AlphaFold monomer V2.0 prediction for glycogen synthase 1 (P0A3F3) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P0A3F3
- Elsewhere: RCSB PDB 1RZU · PDBe 1RZU · UniProt P0A3F3
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