5M5B: Zika virus NS5 methyltransferase

Name: PDB 5M5B: Crystal structure of Zika virus NS5 methyltransferase
Published: 2016-12-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of Zika virus NS5 methyltransferase. Determined by X-ray diffraction at 2.01 Å resolution. Released 28 Dec 2016.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Zika virus
Chains: 2
Atoms: 4,475
Mol. weight: 61.62 kDa
Ligands: SAM
Released: 28 Dec 2016

Explore 5M5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M5B contains 25 α-helices and 20 β-strands across 2 chains. 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: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	14-24	11
α-helix	27-33	7
β-strand	39-42	4	1
α-helix	44-51	8
β-strand	59	1	2
α-helix	64-73	10
β-strand	81-86	6	3
α-helix	92-97	6
β-strand	103-109	7	3
α-helix	117-120	4
α-helix	127-129	3
β-strand	130-133	4	3
α-helix	138-140	3
β-strand	148-151	4	3
α-helix	160-178	19
β-strand	184-189	6	3
α-helix	195-208	14
β-strand	211-213	3	3
β-strand	225-228	4	3
α-helix	235-248	14
α-helix	253-257	5
β-strand	258-261	4	1
α-helix	262-263	2
β-strand	264	1	2

Chain B: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	14-24	11
α-helix	27-35	9
β-strand	39-41	3	4
α-helix	60-63	4
α-helix	66-73	8
β-strand	81-86	6	5
α-helix	92-97	6
β-strand	103-109	7	5
α-helix	127-129	3
β-strand	130-133	4	5
α-helix	138-140	3
α-helix	142-143	2
β-strand	148-151	4	5
α-helix	160-178	19
β-strand	184-189	6	5
α-helix	195-208	14
β-strand	211-213	3	5
β-strand	225-228	4	5
α-helix	235-248	14
α-helix	254-257	4
β-strand	258-260	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NS5 methyltransferase	A, B	protein	272	Zika virus	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5M5B_1 NS5 methyltransferase (chains A, B)
MKHHHHHHGSGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHA
VSRGSAKLRWLVERGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPM
LVQSYGWNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEK
RPGAFCIKVLCPYTSTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVS
TTSQLLLGRMDGPRRPVKYEEDVNLGSGTRAV

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1

Water and common crystallization additives (CL, GOL, SO4) are not listed.

Primary citation

Zika Virus Methyltransferase: Structure and Functions for Drug Design Perspectives. Coutard, B., Barral, K., Lichiere, J. et al. J Virol (2017) 91. DOI 10.1128/JVI.02202-16 · 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
5Y6N 1.57 Å, Zika virus helicase in complex with ADP
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

Browse structure collections

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