Research workbench
Crystal structure of human glycogenin-1 (GYG1) complexed with manganese and glucose or a glucal species
Analyse Crystal structure of human glycogenin-1 (GYG1) complexed with manganese and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U2W
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogenin-1
- EC
- 2.4.1.186
- UniProt
- P46976
- Ligands
- UDP, LCN, GLC, MN
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogenin-1 (EC 2.4.1.186) | protein | 262 | 42% helix, 18% strand | P46976 |
| B | Glycogenin-1 (EC 2.4.1.186) | protein | 253 | 43% helix, 19% strand | P46976 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- LCN · 1,5-anhydro-D-arabino-hex-1-enitol · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.83 | 0.85 | 94 | MN, UDP, GOL, GLC, LCN |
| 2 | 217 | 0.58 | 0.80 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 1349 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3U2W · Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and glucose or a… · the same entry in another collection · chain A against A, TM-score 1.00
- P46976 · AlphaFold monomer V2.0 prediction for glycogenin-1 (P46976) · 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 P46976
- Elsewhere: RCSB PDB 3U2W · PDBe 3U2W · UniProt P46976
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