5Y6N: Zika virus helicase

Zika virus helicase in complex with ADP. Determined by X-ray diffraction at 1.57 Å resolution. Released 4 Jul 2018.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Zika virus (strain Mr 766)
Chains: 1
Atoms: 3,785
Mol. weight: 49.82 kDa
Ligands: ADP, MN
Released: 4 Jul 2018

Explore 5Y6N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y6N contains 27 α-helices and 19 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.

Chain A: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	183-185	3
β-strand	189-192	4	1
α-helix	194-195	2
α-helix	200-204	5
α-helix	205-214	10
β-strand	219-223	5	1
α-helix	226-235	10
β-strand	241-243	3	1
β-strand	258-262	5	1
α-helix	263-271	9
β-strand	281-285	5	1
α-helix	292-306	15
β-strand	311-315	5	1
β-strand	333-337	5	2
α-helix	339-341	3
α-helix	350-353	4
β-strand	359-362	4	2
α-helix	366-378	13
β-strand	383-386	4	2
α-helix	391-395	5
α-helix	396-399	4
β-strand	405-408	4	2
α-helix	410-413	4
β-strand	422-425	4	2
β-strand	428-435	8	3
β-strand	439-447	9	3
α-helix	448-449	2
α-helix	450-457	8
β-strand	469-473	5	2
α-helix	481-483	3
α-helix	485-494	10
α-helix	500-502	3
α-helix	505-508	4
α-helix	509-514	6
α-helix	526-537	12
α-helix	543-551	9
α-helix	560-562	3
α-helix	567-569	3
α-helix	570-571	2
β-strand	572-573	2	4
β-strand	576-577	2	4
β-strand	579-581	3	5
β-strand	587-589	3	5
β-strand	595-596	2	3
α-helix	597-599	3
α-helix	603-613	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Helicase domain from Genome polyprotein	A	protein	438	Zika virus (strain Mr 766)	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5Y6N_1 Helicase domain from Genome polyprotein (chains A)
EPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAEMEEALRGL
PVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTDPSSIAARG
YISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDHSGKT
VWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDISEMGANFK
ADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRGRIGRNPNKPGDEYLYGGGCAE
TDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGEFKLRTEQRKTFVELMKRG
DLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKPRWMDARV
CSDHAALKSFKEFAAGKR

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MN	Manganese (II) ion	Mn	1

Primary citation

Mechanism of ATP hydrolysis by the Zika virus helicase. Yang, X., Chen, C., Tian, H. et al. FASEB J (2018) 32:5250-5257. DOI 10.1096/fj.201701140R · PubMed

Other PDB entries of the same protein (UniProt A0A024B7W1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KQR 1.33 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine
6LD1 1.4 Å, Zika NS5 polymerase domain
6LD2 1.4 Å, Zika NS5 polymerase domain
5KQS 1.5 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and…
6LD4 1.5 Å, Zika NS5 polymerase domain
6S0J 1.5 Å, Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-
5ULP 1.55 Å, Structure of the NS5 methyltransferase from Zika bound to MS2042
7M1V 1.6 Å, Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the…
5KVE 1.7 Å, Zika specific antibody, ZV-48, bound to ZIKA envelope DIII
6RWZ 1.7 Å, Structure of Zika virus NS3 helicase in complex with ADP-BeF3
5JMT 1.8 Å, Crystal structure of Zika virus NS3 helicase
5MRK 1.9 Å, Structural basis of Zika virus methyltransferase inhibition by sinefungin

Browse structure collections

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