MolNFT v1 · #112926 · protein
O-glcnac transferase from drososphila melanogaster
5A01 · O-glycosyltransferase: “O-glcnac transferase from drososphila melanogaster”. X-ray diffraction, 1 ligand (12V), 20 pockets (best druggability 0.76). MolNFT v1 #112926 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5A01
- Type
- protein
- Length
- 2,043 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glycosyltransferase
- EC
- 2.4.-.-, 2.4.1.-, 2.4.1.255
- UniProt
- Q7KJA9
- Ligands
- 12V
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | O-glycosyltransferase (EC 2.4.-.-, 2.4.1.-, 2.4.1.255) | protein | 681 | 50% helix, 14% strand | Q7KJA9 |
Ligands and binding sites
- 12V · (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S, 4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3, 4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.76 | 0.78 | 93 | 12V |
| 2 | 1149 | 0.76 | 0.78 | 99 | 12V |
| 3 | 425 | 0.74 | 0.84 | 52 | empty |
| 4 | 55 | 0.72 | 0.99 | 16 | empty |
| 5 | 57 | 0.72 | 0.98 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 559 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5A01 · O-GlcNAc transferase from Drososphila melanogaster · the same entry in another collection · chain A against A, TM-score 1.00
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 Q7KJA9
- Elsewhere: RCSB PDB 5A01 · PDBe 5A01 · UniProt Q7KJA9
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