5KQS: NS5 methyltransferase from Zika virus

Name: PDB 5KQS: Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and 7-methyl-guanosine-5'-diphosphate
Published: 2016-09-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and 7-methyl-guanosine-5'-diphosphate. Determined by X-ray diffraction at 1.5 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Zika virus (strain Mr 766)
Chains: 1
Atoms: 2,378
Mol. weight: 30.92 kDa
Ligands: PO4, SAM, M7G
Released: 14 Sept 2016

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

Secondary structure: helices and β-sheets

5KQS contains 14 α-helices and 11 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: 14 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-29	9
β-strand	33-35	3	1
α-helix	38-45	8
β-strand	53	1	2
α-helix	58-67	10
β-strand	75-80	6	3
α-helix	86-91	6
β-strand	97-103	7	3
α-helix	111-114	4
α-helix	121-123	3
β-strand	124-127	4	3
α-helix	132-134	3
α-helix	136-137	2
β-strand	142-145	4	3
α-helix	154-172	19
β-strand	178-183	6	3
α-helix	189-202	14
β-strand	205-207	3	3
β-strand	219-222	4	3
α-helix	229-242	14
α-helix	248-251	4
β-strand	252-254	3	1
α-helix	255-257	3
β-strand	258	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Methyltransferase	A	protein	268	Zika virus (strain Mr 766)	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5KQS_1 Methyltransferase (chains A)
GSGGGTGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRG
SAKLRWLVERGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPMLVQS
YGWNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGA
FCIKVLCPYTSTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQ
LLLGRMDGPRRPVKYEEDVNLGSGTRAV

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
M7G	7N-methyl-8-hydroguanosine-5'-diphosphate	C11 H18 N5 O11 P2	1

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

Primary citation

Structures of NS5 Methyltransferase from Zika Virus. Coloma, J., Jain, R., Rajashankar, K.R. et al. Cell Rep (2016) 16:3097-3102. DOI 10.1016/j.celrep.2016.08.091 · 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
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
5MRK 1.9 Å, Structural basis of Zika virus methyltransferase inhibition by sinefungin

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