Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex II). Determined by X-ray diffraction at 2.08 Å resolution. Released 30 Sept 2015.
Explore 4WMK in 3D Show helices and sheets RCSB PDB PDBe
4WMK contains 26 α-helices and 14 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 95 | 1 | |
| β-strand | 96-103 | 8 | 1 |
| α-helix | 111-127 | 17 | |
| β-strand | 134-142 | 9 | 1 |
| α-helix | 144-157 | 14 | |
| β-strand | 165-172 | 8 | 1 |
| α-helix | 173-184 | 12 | |
| α-helix | 185-187 | 3 | |
| α-helix | 188-191 | 4 | |
| α-helix | 199-202 | 4 | |
| α-helix | 203-209 | 7 | |
| α-helix | 210-213 | 4 | |
| β-strand | 220-224 | 5 | 1 |
| β-strand | 228-230 | 3 | 2 |
| α-helix | 234-243 | 10 | |
| α-helix | 244-245 | 2 | |
| β-strand | 250-254 | 5 | 1 |
| α-helix | 255 | 1 | |
| α-helix | 259-263 | 5 | |
| α-helix | 265-270 | 6 | |
| β-strand | 276 | 1 | 3 |
| α-helix | 278-279 | 2 | |
| β-strand | 284 | 1 | 3 |
| β-strand | 287-295 | 9 | 1 |
| α-helix | 296-301 | 6 | |
| α-helix | 303-308 | 6 | |
| α-helix | 311-321 | 11 | |
| α-helix | 329-339 | 11 | |
| α-helix | 341-343 | 3 | |
| β-strand | 344-347 | 4 | 1 |
| α-helix | 348 | 1 | |
| α-helix | 349-351 | 3 | |
| β-strand | 353-354 | 2 | 2 |
| α-helix | 358-362 | 5 | |
| α-helix | 365-372 | 8 | |
| β-strand | 380-382 | 3 | 2 |
| α-helix | 387-390 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 53 | 1 | 4 |
| β-strand | 62 | 1 | 4 |
| α-helix | 73-74 | 2 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Xyloside xylosyltransferase 1 | A | protein | 306 | Mus musculus | Q3U4G3 (AlphaFold model) |
| Coagulation factor IX | D | protein | 50 | Homo sapiens | P00740 (AlphaFold model) |
>4WMK_1 Xyloside xylosyltransferase 1 (chains A) SLEGGVVVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEAS REVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYSDSIFFL SVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQ FRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGH LGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCN TPIPED
>4WMK_2 Coagulation factor IX (chains D) MDIVDGDQCESNPCLNGGSCKDDINSYECWCPFGFEGKNCELLEHHHHHH
Water and common crystallization additives (SO4) are not listed.
Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism. Yu, H., Takeuchi, M., LeBarron, J. et al. Nat Chem Biol (2015) 11:847-854. DOI 10.1038/nchembio.1927 · PubMed
Other PDB entries of the same protein (UniProt Q3U4G3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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