MolNFT v1 · #152242 · protein
Catalytic deficiency of O-glcnac transferase leads to X-linked intellectual disability
6IBO · Udp-N-acetylglucosamine--peptide N…: “Catalytic deficiency of O-glcnac transferase leads to X-linked intellectual disability”. X-ray diffraction, 2 ligands (12V, PO4), 7 pockets (best druggability 0.78). MolNFT v1 #152242 on…
- PDB
- 6IBO
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit…
- EC
- 2.4.1.255
- UniProt
- O15294
- Ligands
- 12V, PO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kda subunit (EC 2.4.1.255) | protein | 695 | 52% helix, 13% strand | O15294 |
| C | Ala-val-ser-arg-ala | protein | 5 | 0% helix, 0% strand | — |
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 · chains A, C
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.78 | 0.89 | 42 | 12V |
| 2 | 889 | 0.73 | 0.77 | 85 | empty |
| 3 | 53 | 0.72 | 0.99 | 17 | empty |
| 4 | 147 | 0.55 | 0.81 | 24 | empty |
| 5 | 116 | 0.39 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 408 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6IBO · Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability · the same entry in another collection · chain A against A, TM-score 1.00
- O15294 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine-- peptide… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O15294
- Elsewhere: RCSB PDB 6IBO · PDBe 6IBO · UniProt O15294
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