1R6A: Dengue virus 2'O methyltransferase

Name: PDB 1R6A: Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate
Published: 2004-09-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of the dengue virus 2'O methyltransferase in complex with s-adenosyl homocysteine and ribavirin 5' triphosphate. Determined by X-ray diffraction at 2.6 Å resolution. Released 21 Sept 2004.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Dengue virus 2 Puerto Rico/PR159-S1/1969
Chains: 1
Atoms: 2,197
Mol. weight: 34.53 kDa
Ligands: SAH, RVP
Released: 21 Sept 2004

Explore 1R6A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1R6A contains 12 α-helices and 9 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: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	10-18	9
α-helix	22-29	8
β-strand	34-37	4	1
α-helix	39-46	8
α-helix	58-66	9
β-strand	75-80	6	2
α-helix	86-91	6
β-strand	97-103	7	2
α-helix	121-123	3
β-strand	124-127	4	2
α-helix	132-134	3
α-helix	136-139	4
β-strand	142-145	4	2
α-helix	154-169	16
β-strand	177-182	6	2
α-helix	188-201	14
β-strand	204-206	3	2
β-strand	218-221	4	2
α-helix	228-241	14
β-strand	251-254	4	1
α-helix	255-256	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A	protein	295	Dengue virus 2 Puerto Rico/PR159-S1/1969	P12823

Sequence of entity 1 (A), FASTA

>1R6A_1 Genome polyprotein (chains A)
GSNIGETLGEKWKSRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSRGSAK
LRWFVERNLVTPEGKVVDLGCGRGGWSYYCGGLKNVREVKGLTKGGPGHEEPIPMSTYGW
NLVRLQSGVDVFFIPPERCDTLLCDIGESSPNPTVEAGRTLRVLNLVENWLSNNTQFCVK
VLNPYMPSVIEKMEALQRKHGGALVRNPLSRNSTHEMYWVSNASGNIVSSVNMISRMLIN
RFTMRHKKATYEPDVDLGSGTRNIGIESETPNLDIIGKRIEKIKQEHETSWHYDQ

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
RVP	Ribavirin monophosphate	C8 H13 N4 O8 P	1

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

Primary citation

A structural basis for the inhibition of the NS5 dengue virus mRNA 2'-O-methyltransferase domain by ribavirin 5'-triphosphate. Benarroch, D., Egloff, M.P., Mulard, L. et al. J Biol Chem (2004) 279:35638-35643. DOI 10.1074/jbc.M400460200 · PubMed

Other PDB entries of the same protein (UniProt P12823), best resolution first:

4M9K 1.46 Å, NS2B-NS3 protease from dengue virus at pH 5.5
4M9M 1.53 Å, NS2B-NS3 protease from dengue virus at pH 8.5
4M9T 1.74 Å, NS2B-NS3 protease from dengue virus in the presence of DTNB, a covalent allosteric…
2P41 1.8 Å, Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG2'OMe and…
1OK8 2.0 Å, Crystal structure of the dengue 2 virus envelope glycoprotein in the postfusion…
2P3L 2.2 Å, Crystal Structure of Dengue Methyltransferase in Complex with GpppA and…
5HHG 2.2 Å, Mouse importin alpha: Dengue 2 NS5 C-terminal NLS peptide complex
1L9K 2.4 Å, dengue methyltransferase
1OKE 2.4 Å, Crystal structure of the dengue 2 virus envelope protein in complex with…
4M9I 2.4 Å, A125C NS2B-NS3 protease from dengue virus at pH 5.5
4M9F 2.7 Å, Dengue virus NS2B-NS3 protease A125C variant at pH 8.5
2P40 2.7 Å, Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG

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