Structure of PDB 5jjr Chain A

Receptor sequence

>5jjrA (length=845) Species: 11069 (dengue virus type 3)

ETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVS
RGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKG
GPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTV
EESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVR
NPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVD
LGAGTRHVNAEPETPNMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHG
SYEVKATGSASSMINGVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKE
KVDTRTPRPLPGTRKVMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTWD
SAKAAVEDEEFWKLVDRERELHKLGKCGSCVYNMMGSRAIWYMWLGVRYL
EFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADD
TAGWDTRITEDDLHNEEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPT
PTGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADL
ENPHLLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALND
MGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDE
LIGRARISSLRETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWV
PTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPY
LGKREDQWCGSLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYM

3D structure

• PDB: 5jjr Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling
• Chain: A
• Resolution: 1.99 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  3.4.21.91: flavivirin.
  3.6.1.15: nucleoside-triphosphate phosphatase.
  3.6.4.13: RNA helicase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ZN	A	E437 H441 C446 C449	E418 H422 C427 C430
BS02	ZN	A	H712 H714 C728 C847	H679 H681 C695 C809
BS03	SAH	A	S56 G58 G81 G86 W87 T104 K105 H110 E111 D131 V132 F133 D146	S50 G52 G75 G80 W81 T98 K99 H104 E105 D125 V126 F127 D140
BS04	68E	A	L511 C709 S710 H711 R729 R737 M761 M765 T794 S796 H798 A799 H800 Q802 W803	L478 C676 S677 H678 R696 R704 M723 M727 T756 S758 H760 A761 H762 Q764 W765	MOAD: ic50=0.016uM PDBbind-CN: -logKd/Ki=7.80,IC50=0.016uM
BS05	MG	A	D533 D664	D500 D631

Gene Ontology

Molecular Function

• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
• GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
• GO:0005524 ATP binding
• GO:0008168 methyltransferase activity

Biological Process

• GO:0032259 methylation
• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:5jjr, PDBe:5jjr, PDBj:5jjr
• PDBsum: 5jjr
• PubMed: 27500641
• UniProt: Q6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)