CpOGA D298N in complex with TAB1-derived O-GlcNAc peptide. Determined by X-ray diffraction at 2.55 Å resolution. Released 14 Mar 2012.
Explore 2YDS in 3D Show helices and sheets RCSB PDB PDBe
2YDS contains 32 α-helices and 23 β-strands across 1 chain. 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 | 42-45 | 4 | |
| α-helix | 49-50 | 2 | |
| β-strand | 52-61 | 10 | 1 |
| α-helix | 62-63 | 2 | |
| β-strand | 65-66 | 2 | 2 |
| β-strand | 67-69 | 3 | 1 |
| α-helix | 76-88 | 13 | |
| β-strand | 92-93 | 2 | 2 |
| α-helix | 94 | 1 | |
| β-strand | 103-108 | 6 | 1 |
| α-helix | 114-119 | 6 | |
| α-helix | 129 | 1 | |
| β-strand | 133-138 | 6 | 1 |
| β-strand | 141-146 | 6 | 1 |
| α-helix | 149-162 | 14 | |
| β-strand | 164 | 1 | 1 |
| β-strand | 167-175 | 9 | 1 |
| β-strand | 181-186 | 6 | 3 |
| α-helix | 192-194 | 3 | |
| α-helix | 195-207 | 13 | |
| β-strand | 212-215 | 4 | 3 |
| α-helix | 230-232 | 3 | |
| α-helix | 233-248 | 16 | |
| β-strand | 252-257 | 6 | 3 |
| α-helix | 267-285 | 19 | |
| β-strand | 291-295 | 5 | 3 |
| α-helix | 304-314 | 11 | |
| α-helix | 315-320 | 6 | |
| α-helix | 321-322 | 2 | |
| α-helix | 325-328 | 4 | |
| β-strand | 329-331 | 3 | 3 |
| α-helix | 337-340 | 4 | |
| β-strand | 341-342 | 2 | 4 |
| β-strand | 345-346 | 2 | 4 |
| α-helix | 348-356 | 9 | |
| β-strand | 362-365 | 4 | 3 |
| β-strand | 375 | 1 | 5 |
| α-helix | 377-387 | 11 | |
| β-strand | 391-395 | 5 | 3 |
| β-strand | 415 | 1 | 5 |
| α-helix | 419-421 | 3 | |
| β-strand | 423-428 | 6 | 3 |
| α-helix | 434-449 | 16 | |
| α-helix | 456-468 | 13 | |
| α-helix | 469-471 | 3 | |
| α-helix | 472-479 | 8 | |
| β-strand | 485-486 | 2 | 6 |
| β-strand | 492-493 | 2 | 6 |
| α-helix | 496 | 1 | |
| α-helix | 499-513 | 15 | |
| α-helix | 519-542 | 24 | |
| α-helix | 545-576 | 32 | |
| α-helix | 580-599 | 20 | |
| α-helix | 606-610 | 5 | |
| α-helix | 611-616 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| O-glcnacase nagj | A | protein | 590 | CLOSTRIDIUM PERFRINGENS | Q0TR53 (AlphaFold model) |
| Tgf-beta-activated kinase 1 and MAP3K7-binding protein 1 | T | protein | 7 | HOMO SAPIENS | Q15750 (AlphaFold model) |
>2YDS_1 O-GLCNACASE NAGJ (chains A) GSVGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTA NNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKD GDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGEN KLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGD AGEEDFNHLITKAESLYDMGVRSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPL ITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYD RNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYS WNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDEL WNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKAS LDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALS
>2YDS_2 TGF-BETA-ACTIVATED KINASE 1 AND MAP3K7-BINDING PROTEIN 1 (chains T) VPYSSAQ
Synergy of Peptide and Sugar in O-Glcnacase Substrate Recognition. Schimpl, M., Borodkin, V.S., Gray, L.J. et al. Chem Biol (2012) 19:173. DOI 10.1016/J.CHEMBIOL.2012.01.011 · PubMed
Other PDB entries of the same protein (UniProt Q0TR53 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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