Structure of PDB 1rtl Chain A

Receptor sequence

>1rtlA (length=180)

APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCING
VCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCG
SSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHA
VGLFRAAVCTRGVTKAVDFIPVENLETTMR

3D structure

• PDB: 1rtl Pyrrolidine-5,5-trans-lactams. 4. Incorporation of a P3/P4 urea leads to potent intracellular inhibitors of hepatitis C virus NS3/4A protease
• Chain: A
• Resolution: 2.75 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D81 G137 S139
• Catalytic site (residue number reindexed from 1): H57 D81 G137 S139
• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  3.4.21.98: hepacivirin.
  3.4.22.-
  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	peptide	A	T4 A5 Y6 A7 Q8 Q9 T10 R11 T19 S20 E30 E32 V33 Q34 I35 V36 S37 R62 T63 I64 A65 W85 R109	T4 A5 Y6 A7 Q8 Q9 T10 R11 T19 S20 E30 E32 V33 Q34 I35 V36 S37 R62 T63 I64 A65 W85 R109
BS02	peptide	A	T4 A5 Y6	T4 A5 Y6
BS03	ZN	A	C97 C99 C145	C97 C99 C145
BS04	CPX	A	Q41 H57 I132 S139 F154 A156 A157	Q41 H57 I132 S139 F154 A156 A157	PDBbind-CN: -logKd/Ki=5.59,IC50=2.6uM

Gene Ontology

Molecular Function

• GO:0008236 serine-type peptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0019087 transformation of host cell by virus

External links

• PDB: RCSB:1rtl, PDBe:1rtl, PDBj:1rtl
• PDBsum: 1rtl
• PubMed: 14627400
• UniProt: P26664|POLG_HCV1 Genome polyprotein