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Crystal structure of human glycogenin-1 (GYG1) complexed with manganese, udp and maltohexaose
Analyse Crystal structure of human glycogenin-1 (GYG1) complexed with manganese, udp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U2V
- Type
- protein
- Length
- 526 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, GLC, MN, SO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycogenin-1 (EC 2.4.1.186) | protein | 263 | 45% helix, 18% strand | P46976 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 12 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.82 | 0.83 | 103 | GLC, UDP |
| 2 | 109 | 0.41 | 0.76 | 16 | empty |
| 3 | 82 | 0.38 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1457 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (glycosylation).
Compared structures
- 3U2V · Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese, UDP and… · 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 0.99
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 3U2V · PDBe 3U2V · UniProt P46976
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