Structure of PDB 4hdh Chain A

Receptor sequence

>4hdhA (length=613) Species: 11072 (Japanese encephalitis virus)

SNQEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVV
KLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLN
ETTNWLWAHLSREKRPRLCTKEEFIKKVNSNAALGAVFAEQNQWSTAREA
VNDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIW
FMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGK
QGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRH
KVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLME
AEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDD
RFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGR
SIVVPCRGQDELIGRARISPGAGWNVKDTACLAKAYAQMWLLLYFHRRDL
RLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENE
WMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRA
VIGKENYVDYMTS

3D structure

• PDB: 4hdh RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state.
• Chain: A
• Resolution: 2.28 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	ATP	A	K463 R474 S666 G667 D668 C714 S715 R734 R742 S799 W800 S801	K186 R197 S389 G390 D391 C437 S438 R457 R465 S522 W523 S524
BS02	ZN	A	E440 H444 C449 C452	E163 H167 C172 C175
BS03	ZN	A	H717 C733 C852	H440 C456 C575

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:4hdh, PDBe:4hdh, PDBj:4hdh
• PDBsum: 4hdh
• PubMed: 24293643
• UniProt: P27395|POLG_JAEV1 Genome polyprotein