Research workbench
Crystal structure of the O-glcnac transferase ASN648TYR mutation
Analyse Crystal structure of the O-glcnac transferase ASN648TYR mutation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q4M
- Type
- protein
- Length
- 698 residues
- Chains
- 1
- 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
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 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 | 698 | 52% helix, 12% strand | O15294 |
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
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.70 | 0.80 | 51 | 12V |
| 2 | 609 | 0.66 | 0.76 | 54 | empty |
| 3 | 164 | 0.62 | 0.84 | 25 | empty |
| 4 | 112 | 0.40 | 0.76 | 23 | empty |
| 5 | 121 | 0.39 | 0.75 | 19 | empty |
Compared structures
- 6Q4M · Crystal structure of the O-GlcNAc transferase Asn648Tyr mutation · 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 0.98
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 O15294
- Elsewhere: RCSB PDB 6Q4M · PDBe 6Q4M · UniProt O15294
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