Zika NS5 polymerase domain. Determined by X-ray diffraction at 1.4 Å resolution. Released 12 Aug 2020.
Explore 6LD2 in 3D Show helices and sheets RCSB PDB PDBe
6LD2 contains 40 α-helices and 18 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 | 275-288 | 14 | |
| β-strand | 294 | 1 | 1 |
| β-strand | 305-311 | 7 | 1 |
| α-helix | 324-328 | 5 | |
| α-helix | 331-333 | 3 | |
| α-helix | 337-340 | 4 | |
| α-helix | 352-355 | 4 | |
| α-helix | 356-360 | 5 | |
| α-helix | 365-368 | 4 | |
| α-helix | 369-386 | 18 | |
| α-helix | 394-396 | 3 | |
| α-helix | 397-404 | 8 | |
| α-helix | 430-445 | 16 | |
| β-strand | 453-456 | 4 | 1 |
| β-strand | 475-477 | 3 | 1 |
| α-helix | 480-490 | 11 | |
| α-helix | 492-495 | 4 | |
| α-helix | 501-504 | 4 | |
| β-strand | 507 | 1 | 2 |
| α-helix | 513-524 | 12 | |
| β-strand | 531 | 1 | 3 |
| β-strand | 532 | 1 | 2 |
| α-helix | 534-535 | 2 | |
| β-strand | 536 | 1 | 4 |
| α-helix | 539-542 | 4 | |
| α-helix | 545-551 | 7 | |
| α-helix | 552-557 | 6 | |
| α-helix | 560-569 | 10 | |
| α-helix | 570-574 | 5 | |
| β-strand | 577-582 | 6 | 1 |
| β-strand | 591-597 | 7 | 1 |
| α-helix | 608-627 | 20 | |
| α-helix | 633-635 | 3 | |
| α-helix | 643-658 | 16 | |
| β-strand | 660-663 | 4 | 2 |
| β-strand | 666-669 | 4 | 2 |
| α-helix | 674-678 | 5 | |
| α-helix | 681-685 | 5 | |
| α-helix | 689 | 1 | |
| β-strand | 690 | 1 | 4 |
| α-helix | 698-699 | 2 | |
| β-strand | 702 | 1 | 3 |
| α-helix | 705-707 | 3 | |
| β-strand | 710 | 1 | 5 |
| β-strand | 713 | 1 | 5 |
| β-strand | 714-719 | 6 | 6 |
| β-strand | 725-730 | 6 | 6 |
| α-helix | 733-740 | 8 | |
| α-helix | 750-767 | 18 | |
| α-helix | 772-784 | 13 | |
| α-helix | 789-791 | 3 | |
| α-helix | 811-816 | 6 | |
| α-helix | 817-821 | 5 | |
| α-helix | 830-832 | 3 | |
| α-helix | 835-837 | 3 | |
| α-helix | 843-848 | 6 | |
| α-helix | 856-863 | 8 | |
| α-helix | 865-876 | 12 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| RNA-directed RNA polymerase NS5 | A | protein | 645 | Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) | A0A024B7W1 (AlphaFold model) |
>6LD2_1 RNA-directed RNA polymerase NS5 (chains A) MHHHHHHSSGVDLGTENLYFQSMAEAPNMKIIGNRIERIRSEHAETWFFDENHPYRTWAY HGSYEAPTQGSASSLINGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKVDTRVPD PQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEWKTAVEA VNDPRFWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWLGARFLE FEALGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWDTRISRF DLENEALITNQMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQDQRGSGQV VTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRRSEKVTNWLQSNGWDRLKRMAVSGDD CVVKPIDDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHHFNKLHLKDGRSI VVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSSVP VDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKRED LWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLSTQVR
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 2 |
| KY3 | (1S,2S,4S,5R)-2,4-dimethoxy-5-thiophen-2-yl-cyclohexane-1-carboxylic acid | C13 H18 O4 S | 1 |
Non-nucleoside Inhibitors of Zika Virus RNA-Dependent RNA Polymerase. Gharbi-Ayachi, A., Santhanakrishnan, S., Wong, Y.H. et al. J Virol (2020) 94. DOI 10.1128/JVI.00794-20 · PubMed
Other PDB entries of the same protein (UniProt A0A024B7W1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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