Structure of PDB 5i3p Chain A

Receptor sequence

>5i3pA (length=585) Species: 11069 (dengue virus type 3)

NMDVIGERIKRIKEEHNSTWHYDDENPYKTWAYHGSYEVKATGSASSMIN
GVVKLLTKPWDVVPMVTQMAMTDTTPFGQQRVFKEKVDTRTPRPLPGTRK
VMEITAEWLWRTLGRNKRPRLCTREEFTKKVRTNAADSAKAAVEDEEFWK
LVDRERELHKLGKCGSCVYNMSRAIWYMWLGVRYLEFEALGFLNEDHWFS
RENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHN
EEKIIQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPTGTVMDIISRKDQR
GSGQVGTYGLNTFTNMEAQLVRQMEGEGVLTKADLENPHLLEKKITQWLE
TKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSK
GWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSL
RETACLGKAYAQMWSLMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIH
AHHQWMTTEDMLTVWNRVWIEENPWMEDKTPVTTWENVPYLGKREDQWCG
SLIGLTSRATWAQNIPTAIQQVRSLIGNEEFLDYM

3D structure

• PDB: 5i3p Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling
• Chain: A
• Resolution: 2.45 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	H712 H714 C728 C847	H414 H416 C430 C549
BS02	ZN	A	E437 H441 C446 C449	E155 H159 C164 C167
BS03	68T	A	L511 C709 S710 R729 R737 M761 M765 T794 S796 H798 A799 H800 Q802 W803	L213 C411 S412 R431 R439 M463 M467 T496 S498 H500 A501 H502 Q504 W505

Gene Ontology

Molecular Function

• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005524 ATP binding

Biological Process

• GO:0039694 viral RNA genome replication

External links

• PDB: RCSB:5i3p, PDBe:5i3p, PDBj:5i3p
• PDBsum: 5i3p
• PubMed: 27500641
• UniProt: Q6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)