MolNFT v1 · #76784 · protein
Crystal structure of human glycogenin-1 (GYG1) complexed with manganese and udp
3QVB: “Crystal structure of human glycogenin-1 (GYG1) complexed with manganese and udp”. X-ray diffraction, 2 ligands (UDP, MN), 2 pockets (best druggability 0.49). MolNFT v1 #76784 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3QVB
- Type
- protein
- Length
- 251 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogenin-1
- EC
- 2.4.1.186
- UniProt
- P46976
- Ligands
- UDP, MN
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogenin-1 (EC 2.4.1.186) | protein | 251 | 41% helix, 20% strand | P46976 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.49 | 0.77 | 25 | UDP |
| 2 | 93 | 0.37 | 0.75 | 19 | empty |
Compared structures
- 3QVB · Crystal Structure of Human Glycogenin-1 (GYG1) complexed with manganese and UDP · 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 0.93
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 P46976
- Elsewhere: RCSB PDB 3QVB · PDBe 3QVB · UniProt P46976
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