The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678. Determined by X-ray diffraction at 2.43 Å resolution. Released 25 Dec 2019.
Explore 6IZX in 3D Show helices and sheets RCSB PDB PDBe
6IZX contains 41 α-helices and 22 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 | 274-286 | 13 | |
| β-strand | 293 | 1 | 1 |
| β-strand | 304-310 | 7 | 1 |
| α-helix | 319 | 1 | |
| β-strand | 320-321 | 2 | 2 |
| α-helix | 323-328 | 6 | |
| α-helix | 330-334 | 5 | |
| α-helix | 336-340 | 5 | |
| α-helix | 348-354 | 7 | |
| α-helix | 355-359 | 5 | |
| α-helix | 364-367 | 4 | |
| α-helix | 368-385 | 18 | |
| α-helix | 393-395 | 3 | |
| α-helix | 396-403 | 8 | |
| β-strand | 411 | 1 | 3 |
| α-helix | 422-427 | 6 | |
| α-helix | 429-443 | 15 | |
| β-strand | 452-454 | 3 | 1 |
| β-strand | 475-476 | 2 | 1 |
| β-strand | 478 | 1 | 3 |
| α-helix | 479-489 | 11 | |
| α-helix | 491-494 | 4 | |
| α-helix | 500-503 | 4 | |
| β-strand | 506 | 1 | 4 |
| α-helix | 512-523 | 12 | |
| β-strand | 530 | 1 | 5 |
| β-strand | 531 | 1 | 4 |
| α-helix | 533-534 | 2 | |
| β-strand | 535 | 1 | 6 |
| α-helix | 538-541 | 4 | |
| α-helix | 544-551 | 8 | |
| α-helix | 552-556 | 5 | |
| α-helix | 559-567 | 9 | |
| α-helix | 568-573 | 6 | |
| β-strand | 576-584 | 9 | 1 |
| β-strand | 587-595 | 9 | 1 |
| α-helix | 609-625 | 17 | |
| α-helix | 637-655 | 19 | |
| β-strand | 658-661 | 4 | 4 |
| β-strand | 664-667 | 4 | 4 |
| α-helix | 672-676 | 5 | |
| α-helix | 679-683 | 5 | |
| α-helix | 687 | 1 | |
| β-strand | 688 | 1 | 6 |
| α-helix | 696-698 | 3 | |
| β-strand | 700 | 1 | 5 |
| α-helix | 703-705 | 3 | |
| β-strand | 708 | 1 | 7 |
| β-strand | 711 | 1 | 7 |
| β-strand | 712-717 | 6 | 8 |
| β-strand | 723-728 | 6 | 8 |
| α-helix | 731-738 | 8 | |
| β-strand | 740-741 | 2 | 2 |
| α-helix | 748-765 | 18 | |
| α-helix | 770-782 | 13 | |
| α-helix | 788-790 | 3 | |
| α-helix | 809-813 | 5 | |
| α-helix | 814-819 | 6 | |
| α-helix | 828-830 | 3 | |
| α-helix | 837-840 | 4 | |
| α-helix | 841-844 | 4 | |
| α-helix | 853-861 | 9 | |
| α-helix | 863-874 | 12 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Genome polyprotein | A | protein | 686 | Dengue virus 2 | P14340 |
>6IZX_1 Genome polyprotein (chains A) MKDHLIHNHHKHEHAHAEHDYKDDDDKEHLYFQGSSGSSGTYEPDVDLGSGTRNIGIESE IPNLDIIGKRIEKIKQEHETSWHYDQDHPYKTWAYHGSYETKQTGSASSMVNGVVRLLTK PWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTQEPKEGTKKLMKITAEWLWKELGKKKT PRMCTREEFTRKVRSNAALGAIFTDENKWKSAREAVEDSRFWELVDKERNLHLEGKCETC VYNMMGKREKKLGEFGKAKGSRAIWYMWLGARFLEFEALGFLNEDHWFSRENSLSGVEGE GLHKLGYILRDVSKKEGGAMYADDTAGWDTRITLEDLKNEEMVTNHMEGEHKKLAEAIFK LTYQNKVVRVQRPTPRGTVMDIISRRDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGVFK SIQHLTVTEEIAVQNWLARVGRERLSRMAISGDDCVVKPLDDRFASALTALNDMGKVRKD IQQWEPSRGWNDWTQVPFCSHHFHELIMKDGRVLVVPCRNQDELIGRARISQGAGWSLRE TACLGKSYAQMWSLMYFHRRDLRLAANAICSAVPSHWVPTSRTTWSIHAKHEWMTTEDML TVWNRVWIQENPWMEDKTPVESWEEIPYLGKREDQWCGSLIGLTSRATWAKNIQTAINQV RSLIGNEEYTDYMPSMKRFRREEEEA
| ID | Name | Formula | Copies |
|---|---|---|---|
| B5C | 2-oxo-2H-1,3-benzoxathiol-5-yl acetate | C9 H6 O4 S | 2 |
| CO | Cobalt (II) ion | Co | 9 |
| ZN | Zinc ion | Zn | 2 |
Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase. Shimizu, H., Saito, A., Mikuni, J. et al. PLoS Negl Trop Dis (2019) 13:e0007894-e0007894. DOI 10.1371/journal.pntd.0007894 · PubMed
Other PDB entries of the same protein (UniProt P14340), best resolution first:
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