3SU1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NS3/4A PROTEASE VARIANT D168A IN COMPLEX WITH DANOPREVIR

Authors :   C. A. Schiffer, K. P. Romano

Date :   11 Jul 11 (Deposition) - 05 Sep 12 (Release) - 05 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Ns3, Drug Resistance, Drug Design, Protease Inhibitors, Hcv, Serine Protease, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. P. Romano, A. Ali, C. Aydin, D. Soumana, A. Ozen, L. M. Deveau, C. Silver, H. Cao, A. Newton, C. J. Petropoulos, W. Huang, C. A. Schiffe
The Molecular Basis Of Drug Resistance Against Hepatitis C Virus Ns3/4A Protease Inhibitors.
Plos Pathog. V. 8 02832 2012
PubMed-ID: 22910833 | Reference-DOI: 10.1371/JOURNAL.PPAT.1002832

Molecule 1 - GENOME POLYPROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NS3-NS4A
	Organism Scientific	:	HEPATITIS C VIRUS SUBTYPE 1A
	Organism Taxid	:	31646
	Strain	:	BID-V318

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	TSV	1	Ligand/Ion	(2R,6S,12Z,13AS,14AR,16AS)-6-[(TERT-BUTOXYCARBONYL)AMINO]-14A-[(CYCLOPROPYLSULFONYL)CARBAMOYL]-5,16-DIOXO-1,2,3,5,6,7,8,9,10,11,13A,14,14A,15,16,16A-HEXADECAHYDROCYCLOPROPA[E]PYRROLO[1,2-A][1,4]DIAZACYCLOPENTADECIN-2-YL 4-FLUORO-2H-ISOINDOLE-2-CARBOXYLATE
3	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:56 , HOH A:155 , HOH A:161 , HOH A:166 , HIS A:982 , GLN A:1041 , PHE A:1043 , HIS A:1057 , GLY A:1058 , ASP A:1079 , ASP A:1081 , ARG A:1123 , LEU A:1135 , LYS A:1136 , GLY A:1137 , SER A:1138 , ALA A:1139 , PHE A:1154 , ARG A:1155 , ALA A:1156 , ALA A:1157	BINDING SITE FOR RESIDUE TSV A 100
2	AC2	SOFTWARE	HOH A:11 , HOH A:13 , HOH A:57 , HOH A:64 , HOH A:140 , TYR A:1006 , GLN A:1008 , TYR A:1056	BINDING SITE FOR RESIDUE SO4 A 1
3	AC3	SOFTWARE	HOH A:93 , HOH A:133 , HOH A:196 , LYS A:1080 , ARG A:1155 , PRO A:1171 , SER A:1174	BINDING SITE FOR RESIDUE SO4 A 2
4	AC4	SOFTWARE	HOH A:74 , HOH A:120 , HOH A:175 , ARG A:1109 , HIS A:1110	BINDING SITE FOR RESIDUE SO4 A 4
5	AC5	SOFTWARE	HOH A:198 , SER A:1122 , ARG A:1123 , ARG A:1155 , ALA A:1168	BINDING SITE FOR RESIDUE SO4 A 5
6	AC6	SOFTWARE	CYS A:1097 , CYS A:1099 , CYS A:1145 , HIS A:1149	BINDING SITE FOR RESIDUE ZN A 1183

(no "SS Bond" information available for 3SU1)

(no "Cis Peptide Bond" information available for 3SU1)

(no "SAP(SNP)/Variant" information available for 3SU1)

(no "PROSITE Motif" information available for 3SU1)

(no "Exon" information available for 3SU1)

Asymmetric/Biological 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:200
 aligned with A8DG50_9HEPC | A8DG50 from UniProtKB/TrEMBL  Length:3011

    Alignment length:256
                                   960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      
        A8DG50_9HEPC    951 NHLTPLRDWAHNGLQDLAVAVEPVVFSPMETKLITWGADTAACGDIINGLPVSARRGQEILLGPADGVVSKGWRLLAPITAYAQQTRGLLGCIITSLTGRDKNQVEGEVQIVSTAAQTFLATCINGVCWTVYHGAGTRTIASPKGPVIQMYTNVDKDLVGWPAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSSGGPLLCPAGHAVGIFRAAVCTRGVAKAVDFIPVESLETTMR 1206
               SCOP domains d3su1a_                                                A: automate         d matches                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.-----------------------------------------------.....eeeeeee---------......eeee..hhhhhhhhhhhh.........eeeee....eeeeeee..eeeeehhhhh..............eee....eeeee................eeeee.....eeeeee....eeeeeeeee.hhh......eee.....eeeeeeeeeee..eeeeeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3su1 A  981 SHMASMK-----------------------------------------------KKGSVVIVGRIN---------LSGDTAYAQQTRGEEGCQETSQTGRDKNQVEGEVQIVSTATQTFLATSINGVLWTVYHGAGTRTIASPKGPVTQMYTNVDKDLVGWQAPQGSRSLTPCTCGSSDLYLVTRHADVIPVRRRGDSRGSLLSPRPISYLKGSAGGPLLCPAGHAVGIFRAAVSTRGVAKAVAFIPVESLETTMR 1180
                                  |  -         -         -         -         -    |  993     |   -     |1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      
                                987                                             988        999      1000

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Viral proteases (62)

Protein domain: automated matches (23)

Hepatitis C virus subtype 1a [TaxId: 31646] (15)

d3su1a_

(no "CATH Domain" information available for 3SU1)

(no "Pfam Domain" information available for 3SU1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A8DG50_9HEPC | A8DG50)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3su1)

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	3su1
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	A8DG50_9HEPC \| A8DG50	:	5voj 5vp9
UniProtKB/TrEMBL
	A8DG50_9HEPC \| A8DG50	:	3m5l 3m5m 3m5n 3m5o 3rc6 3su0 3su2 3su3 3su4 3su5 3su6 3sud 3sue 3suf 3sug 3sv6 3sv7 3sv8 3sv9 4nwk 4nwl 4wh6 4wh8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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SCOP Domains (1, 1)

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Gene Ontology (31, 31)

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