Complex of a C. perfringens O-GlcNAcase with a fragment hit. Determined by X-ray diffraction at 2.6 Å resolution. Released 16 May 2018.
Explore 5OXD in 3D Show helices and sheets RCSB PDB PDBe
5OXD contains 30 α-helices and 26 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 | 49-50 | 2 | |
| β-strand | 52-55 | 4 | 1 |
| β-strand | 60-61 | 2 | 2 |
| α-helix | 62-63 | 2 | |
| β-strand | 65-69 | 5 | 1 |
| α-helix | 76-88 | 13 | |
| β-strand | 92-93 | 2 | 1 |
| β-strand | 102-108 | 7 | 1 |
| α-helix | 114-120 | 7 | |
| 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 | 2 |
| β-strand | 167-168 | 2 | 2 |
| β-strand | 171-175 | 5 | 1 |
| β-strand | 181-185 | 5 | 3 |
| α-helix | 192-194 | 3 | |
| α-helix | 195-207 | 13 | |
| β-strand | 212-215 | 4 | 3 |
| α-helix | 221-223 | 3 | |
| β-strand | 224 | 1 | 4 |
| β-strand | 226 | 1 | 4 |
| α-helix | 236-248 | 13 | |
| β-strand | 252-257 | 6 | 3 |
| α-helix | 259-261 | 3 | |
| α-helix | 267-285 | 19 | |
| β-strand | 292-295 | 4 | 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 | 5 |
| β-strand | 345-346 | 2 | 5 |
| α-helix | 348-356 | 9 | |
| β-strand | 362-365 | 4 | 3 |
| β-strand | 375 | 1 | 6 |
| α-helix | 377-387 | 11 | |
| β-strand | 391-395 | 5 | 3 |
| β-strand | 415 | 1 | 6 |
| 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 | 7 |
| β-strand | 492-493 | 2 | 7 |
| α-helix | 496 | 1 | |
| α-helix | 499-513 | 15 | |
| α-helix | 519-542 | 24 | |
| α-helix | 545-575 | 31 | |
| α-helix | 580-599 | 20 | |
| α-helix | 609-616 | 8 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| O-GlcNAcase NagJ | A | protein | 590 | Clostridium perfringens | Q0TR53 (AlphaFold model) |
>5OXD_1 O-GlcNAcase NagJ (chains A) GSVGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTA NNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKD GDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGEN KLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGD AGEEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPL ITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYD RNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYS WNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDEL WNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKAS LDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALS
| ID | Name | Formula | Copies |
|---|---|---|---|
| B2W | 5-(trifluoromethyl)-2,3-dihydro-1~{H}-1,4-diazepine | C6 H7 F3 N2 | 1 |
| CD | Cadmium ion | Cd | 22 |
O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry. Borodkin, V.S., Rafie, K., Selvan, N. et al. ACS Chem Biol (2018) 13:1353-1360. DOI 10.1021/acschembio.8b00183 · 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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