Structure of PDB 5f41 Chain A

Receptor sequence

>5f41A (length=585) Species: 11069 (dengue virus type 3)

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

3D structure

• PDB: 5f41 A Conserved Pocket in the Dengue Virus Polymerase Identified through Fragment-based Screening
• Chain: A
• Resolution: 2.0 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	5V6	A	L511 C709 H711 R729 M761 T794 S796 H798 A799 W803	L213 C411 H413 R431 M463 T496 S498 H500 A501 W505	MOAD: Kd=67uM PDBbind-CN: -logKd/Ki=4.17,Kd=67uM

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:5f41, PDBe:5f41, PDBj:5f41
• PDBsum: 5f41
• PubMed: 26872970
• UniProt: Q6YMS4|POLG_DEN3S Genome polyprotein (Gene Name=pol)