Structure of PDB 2o8m Chain A

Receptor sequence

>2o8mA (length=185)

QMGAPITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATC
INGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPC
TCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSAGGPLLCPA
GHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRSG

3D structure

• PDB: 2o8m Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3- [2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]- 6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D81 G137 A139
• Catalytic site (residue number reindexed from 1): H60 D84 G140 A142
• 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	Q-3 T4 A5 Y6 A7 Q8 T10 C16 T19 S20 E30 E32 V33 Q34 I35 V36 S37 R62 T63 I64 A65 R109	Q1 T7 A8 Y9 A10 Q11 T13 C19 T22 S23 E33 E35 V36 Q37 I38 V39 S40 R65 T66 I67 A68 R112
BS02	peptide	A	T4 A5 Y6 A7	T7 A8 Y9 A10
BS03	ZN	A	C97 C99 C145	C100 C102 C148

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:2o8m, PDBe:2o8m, PDBj:2o8m
• PDBsum: 2o8m
• PubMed: 17444623
• UniProt: P27958|POLG_HCV77 Genome polyprotein