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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF NOROVIRUS 3C-LIKE PROTEASE

Authors :   K. Nakamura, Y. Someya, T. Kumasaka, N. Tanaka

Date :   01 Oct 04 (Deposition) - 04 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Crystal Structure, Norovirus, 3C-Like Protease, Chymotrypsin Like Protease, Oxyanion Hole, Norwalk-Like Virus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Nakamura, Y. Someya, T. Kumasaka, G. Ueno, M. Yamamoto, T. Sato, N. Takeda, T. Miyamura, N. Tanaka
A Norovirus Protease Structure Provides Insights Into Active And Substrate Binding Site Integrity
J. Virol. V. 79 13685 2005
PubMed-ID: 16227288 | Reference-DOI: 10.1128/JVI.79.21.13685-13693.2005
(for further references see the PDB file header)

Molecule 1 - 3C-LIKE PROTEASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTYB11
	Expression System Strain	:	BL21(DE3)-CODON-PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-173
	Organism Scientific	:	CHIBA VIRUS
	Organism Taxid	:	99565

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	HG	8	Ligand/Ion	MERCURY (II) ION
2	TAR	1	Ligand/Ion	D(-)-TARTARIC ACID
3	TLA	1	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:77 , CYS A:154 , CYS A:169 , HG A:1002	BINDING SITE FOR RESIDUE HG A 1001
02	AC2	SOFTWARE	CYS A:77 , CYS A:83 , TYR A:145 , CYS A:154 , HG A:1001	BINDING SITE FOR RESIDUE HG A 1002
03	AC3	SOFTWARE	TYR B:143 , CYS B:154 , CYS B:169 , HG B:1004	BINDING SITE FOR RESIDUE HG B 1003
04	AC4	SOFTWARE	CYS B:77 , CYS B:83 , MET B:101 , TYR B:143 , CYS B:154 , HG B:1003	BINDING SITE FOR RESIDUE HG B 1004
05	AC5	SOFTWARE	MET C:101 , CYS C:154 , CYS C:169	BINDING SITE FOR RESIDUE HG C 1005
06	AC6	SOFTWARE	CYS C:77 , CYS C:83 , TYR C:145 , CYS C:154	BINDING SITE FOR RESIDUE HG C 1006
07	AC7	SOFTWARE	MET D:101 , CYS D:154 , CYS D:169 , HG D:1008	BINDING SITE FOR RESIDUE HG D 1007
08	AC8	SOFTWARE	CYS D:77 , CYS D:83 , MET D:101 , CYS D:154 , HG D:1007	BINDING SITE FOR RESIDUE HG D 1008
09	AC9	SOFTWARE	ARG A:89 , ASP A:90 , LEU A:135 , PRO A:136 , GLY A:137 , ASP A:138 , MET C:130	BINDING SITE FOR RESIDUE TLA A 301
10	BC1	SOFTWARE	SER A:14 , HIS A:30 , CYS A:139	BINDING SITE FOR RESIDUE TAR A 300

Asymmetric/Biological Unit

No.	Residues
1	B:77	-	B:154
2	D:83	-	D:154

(no "Cis Peptide Bond" information available for 1WQS)

(no "SAP(SNP)/Variant" information available for 1WQS)

(no "PROSITE Motif" information available for 1WQS)

(no "Exon" information available for 1WQS)

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:173
 aligned with Q9DU47_CHIBA | Q9DU47 from UniProtKB/TrEMBL  Length:1785

    Alignment length:173
                                  1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266   
        Q9DU47_CHIBA   1097 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA 1269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eee....eeee....eeeee.hhh..........hhhhheeeee..eeeee............ee........eeeeeee.....eeeeeeeeeeeeeehhhhh.eeeeeeee....................eeeee....eeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wqs A    1 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q9DU47_CHIBA | Q9DU47 from UniProtKB/TrEMBL  Length:1785

    Alignment length:173
                                  1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266   
        Q9DU47_CHIBA   1097 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA 1269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeee..eeee.....eeee.hhhh.........................ee............ee........eeeeeee.....eeeeeeeeeeeeeee....eeeeeeeee....................eeeee....eeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wqs B    1 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain C from PDB  Type:PROTEIN  Length:173
 aligned with Q9DU47_CHIBA | Q9DU47 from UniProtKB/TrEMBL  Length:1785

    Alignment length:173
                                  1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266   
        Q9DU47_CHIBA   1097 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA 1269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeee..eeeee....eeeee.hhh.....ee..ee.hhheeeee..eeeee............ee........eeeeeee.....eeeeeeeeeeeeee......eeeeeeee.............hhhhh..eeeee....eeeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wqs C    1 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain D from PDB  Type:PROTEIN  Length:173
 aligned with Q9DU47_CHIBA | Q9DU47 from UniProtKB/TrEMBL  Length:1785

    Alignment length:173
                                  1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266   
        Q9DU47_CHIBA   1097 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA 1269
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_C37-1wqsD01 D:1-169                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) Peptidase_C37-1wqsD02 D:1-169                                                                                                                                            ---- Pfam domains (2)
           Pfam domains (3) Peptidase_C37-1wqsD03 D:1-169                                                                                                                                            ---- Pfam domains (3)
           Pfam domains (4) Peptidase_C37-1wqsD04 D:1-169                                                                                                                                            ---- Pfam domains (4)
         Sec.struct. author ...hhhh.eeee..eeeee.....eeee.........ee..ee...........ee.........................eee..ee.....ee..eeee....ee......ee.eeeee.............hhhhh..ee...........eeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wqs D    1 APPTLWSRVVRFGSGWGFWVSPTVFITTTHVIPTGVREFFGEPIESIAIHRAGEFTQFRFSRKVRPDLTGMVLEEGCPEGVVCSILIKRDSGELLPLAVRMGAIASMKIQGRLVHGQSGMLLTGANAKGMDLGTLPGDCGAPYVYKRNNDWVVCGVHAAATKSGNTVVCAVQA  173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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 '\|'

(no "SCOP Domain" information available for 1WQS)

(no "CATH Domain" information available for 1WQS)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Peptidase_C37 (1)

Chiba virus (strain GI/Human/Japan/Chiba 407/1987) (Hu/NLV/Chiba 407/1987/JP) (1)

1a	Peptidase_C37-1wqsD01	D:1-169
1b	Peptidase_C37-1wqsD02	D:1-169
1c	Peptidase_C37-1wqsD03	D:1-169
1d	Peptidase_C37-1wqsD04	D:1-169

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q9DU47_CHIBA | Q9DU47)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003724	RNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
	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:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of 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: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: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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	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.
biological process
	GO:0044419	interspecies interaction between organisms	Any process in which an organism has an effect on an organism of a different species.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0001172	transcription, RNA-templated	The cellular synthesis of RNA on a template of RNA.
	GO:0039694	viral RNA genome replication	The replication of a viral RNA genome.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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