3KNX - JenaLib

Title :   HCV NS3 PROTEASE DOMAIN WITH P1-P3 MACROCYCLIC KETOAMIDE INHIBITOR

Authors :   S. Venkatraman, F. Velazquez, W. Wu, M. Blackman, K. X. Chen, S. Bogen, L X. Tong, R. Chase, A. Hart, S. Agrawal, J. Pichardo, A. Prongay, K. -C. C V. Girijavallabhan, J. Piwinski, N. -Y. Shih, F. G. Njoroge

Date :   12 Nov 09 (Deposition) - 27 Oct 10 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Hepatitis C Virus, Ns3 Protease Domain, Serine Protease, Macrocyclic Ketoamide Inhibitor, Atp-Binding, Envelope Protein, Helicase, Hydrolase, Membrane, Nucleotide-Binding, Rna Replication, Transmembrane, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Venkatraman, F. Velazquez, W. Wu, M. Blackman, K. X. Chen, S. Bogen, L. Nair, X. Tong, R. Chase, A. Hart, S. Agrawal, J. Pichardo, A. Prongay K. C. Cheng, V. Girijavallabhan, J. Piwinski, N. Y. Shih, F. G. Njoroge
Discovery And Structure-Activity Relationship Of P1-P3 Ketoamide Derived Macrocyclic Inhibitors Of Hepatitis C Virus Ns3 Protease.
J. Med. Chem. V. 52 336 2009
PubMed-ID: 19102654 | Reference-DOI: 10.1021/JM800940U

Compounds

Molecule 1 - HCV NS3 PROTEASE
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET-3A
	Fragment	:	PROTEASE DOMAIN, UNP RESIDUES 1027-1207
	Gene	:	NS3
	Organism Scientific	:	HEPATITIS C VIRUS SUBTYPE 1A
	Organism Taxid	:	63746
	Strain	:	H77 STRAIN OF GENOTYPE 1A

Molecule 2 - HCV NS4A PEPTIDE
	Chains	:	B, D
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 1678-1696
	Mutation	:	YES
	Other Details	:	PEPTIDES WERE SYNTHESIZED USING FMOC SOLID-PHASE CHEMISTRY ON AN ABI 431 SYNTHESIZER (FOSTER CITY, CA). PRELOADED 2- CHLOROTRITYL CHLORIDE RESIN OR WANG RESIN WAS USED FOR THE SOLID PHASE ASSEMBLY OF NS4A ACTIVATOR PEPTIDE. THE SEQUENCE OF THE PEPTIDE WAS LYS-LYS-GLY-SER-VAL-VAL-ILE-VAL-GLY-ARG-ILE-ILE-LEU-SER- GLY-ARG-PRO-ALA-ILE-VAL-PRO-LYS-LYS-OH. TRIFUNCTIONAL RESIDUE SIDECHAIN PROTECTING GROUPS INCLUDED TERT-BUTYL FOR SER, TERT- BUTOXYCARBONYL FOR LYS, AND 2,2,4,6,7-PENTAMETHYLDIHYDROBENZOFURAN- 5-SULFONYL FOR ARG. CLEAVAGE AND SIDECHAIN DEPROTECTION WAS ACCOMPLISHED USING 92.5% TRIFLUOROACETIC ACID, WITH 2.5% EACH OF WATER, ETHANEDITHIOL AND TRIISOPROPYLSILANE FOR 2 HOURS. THE PEPTIDE WAS PURIFIED BY REVERSED PHASE HPLC. THE PEPTIDE MOLECULAR WEIGHT WAS CONFIRMED BY ELECTROSPRAY IONIZATION MASS SPECTROMETRY.
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:181
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:181
                                  1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206 
        Q9ELS8_9HEPC   1027 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRQGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRS 1207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh...eee..eee...eee....eeeee................eeeee.....eeeeee....eeeeeeeeehhhhh.....eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3knx A    1 APITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTMRS  181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:22
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:22
                                  1686      1696  
        Q9ELS8_9HEPC   1677 TGCVVIVGRIVLSGKPAIIPDR 1698
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                3knx B   20 KGSVVIVGRIVLSGKPAIIPKK   41
                                    29        39

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:151
                                  1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204 
        Q9ELS8_9HEPC   1055 VEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRQGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM 1205
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Peptidase_S29-3knxC01 C:30-178                                                                                                                       - Pfam domains (1)
           Pfam domains (2) -Peptidase_S29-3knxC02 C:30-178                                                                                                                       - Pfam domains (2)
         Sec.struct. author ....eeeee....eeeeeee..eeeeehhhhh..ee..........eee....eeeee................eeeee.....eeeeeeee..eeeeeeeee.hhhh.....eee.....eeeeeeeeee...eeeeeeeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3knx C   29 VEGEVQIVSTATQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDQDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGLFRAAVCTRGVAKAVDFIPVENLETTM  179
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

Chain D from PDB  Type:PROTEIN  Length:16
 aligned with Q9ELS8_9HEPC | Q9ELS8 from UniProtKB/TrEMBL  Length:3011

    Alignment length:16
                                  1687      
        Q9ELS8_9HEPC   1678 GCVVIVGRIVLSGKPA 1693
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
           Pfam domains (1) --HCV_NS4a-3knxD Pfam domains (1)
           Pfam domains (2) --HCV_NS4a-3knxD Pfam domains (2)
         Sec.struct. author .eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                3knx D   21 GSVVIVGRIVLSGKPA   36
                                    30

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (31, 31)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9ELS8_9HEPC | Q9ELS8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008026	ATP-dependent helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003968	RNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
	GO:0004197	cysteine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0017111	nucleoside-triphosphatase activity	Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0039520	induction by virus of host autophagy	Any process in which a virus activates or increases the frequency, rate or extent of autophagy in the host.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	GO:0019087	transformation of host cell by virus	Any virus-induced change in the morphological, biochemical, or growth parameters of a cell.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0019079	viral genome replication	Any process involved directly in viral genome replication, including viral nucleotide metabolism.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

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