Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CVA16 3C IN COMPLEX WITH RUPINTRIVIR (AG7088)
 
Authors :  G. Lu, J. Qi, Z. Chen, X. Xu, F. Gao, D. Lin, W. Qian, H. Liu, H. Jiang, J. Yan
Date :  21 Jun 11  (Deposition) - 10 Aug 11  (Release) - 28 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  In Complex With Rupintrivir, Chymotrypsin-Like Fold, Protease, C147 Covalently Binds To Rupintrivir, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Lu, J. Qi, Z. Chen, X. Xu, F. Gao, D. Lin, W. Qian, H. Liu, H. Jiang, J. Yan, G. F. Gao
Enterovirus 71 And Coxsackievirus A16 3C Proteases: Binding To Rupintrivir And Their Substrates And Anti-Hand, Foot, An Mouth Disease Virus Drug Design.
J. Virol. V. 85 10319 2011
PubMed-ID: 21795339  |  Reference-DOI: 10.1128/JVI.00787-11

(-) Compounds

Molecule 1 - 3C PROTEASE
    Chains: A
    EC Number: 3.4.22.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-183
    Gene: 3C
    Organism Scientific: HUMAN COXSACKIEVIRUS A16
    Organism Taxid: 31704
    Strain: BEIJING0907

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1AG71Ligand/Ion4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:39 , HIS A:40 , GLN A:66 , GLY A:67 , GLU A:71 , LEU A:125 , ASN A:126 , LEU A:127 , SER A:128 , LYS A:130 , THR A:142 , LYS A:143 , ALA A:144 , GLY A:145 , CYS A:147 , HIS A:161 , ILE A:162 , GLY A:163 , GLY A:164 , ASN A:165 , PHE A:170 , HOH A:226BINDING SITE FOR RESIDUE AG7 A 501
2AC2SOFTWAREPRO A:43 , THR A:46 , GLU A:92 , HOH A:193 , HOH A:370BINDING SITE FOR RESIDUE NA A 191

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SJI)

(-) Sequences/Alignments

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:179
 aligned with C8CIL7_9ENTO | C8CIL7 from UniProtKB/TrEMBL  Length:645

    Alignment length:179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173         
         C8CIL7_9ENTO     4 LDFALSLLRRNIRQVQTDQGHFTMLGVRDRLAILPRHSQPGKTIWVEHKLINVLDAVELVDEQGVNLELTLVTLDTNEKFRDVTKFIPETITGASDATLIINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVTSVGKIIGIHIGGNGRQGFCAGLKRGYFASE 182
               SCOP domains d3sjia_ A: 3C cysteine protease (picornain 3C)                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhheeeeee..eeeeeeeee..eeeee.hhh...eeee..eeeeeeeeeeee.....eeeeeeeee........hhhhh......eeeeeeee.......eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeee....eeeee.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sji A   4 LDFALSLLRRNIRQVQTDQGHFTMLGVRDRLAILPRHSQPGKTIWVEHKLINVLDAVELVDEQGVNLELTLVTLDTNEKFRDVTKFIPETITGASDATLIINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVTSVGKIIGIHIGGNGRQGFCAGLKRGYFASE 182
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C8CIL7_9ENTO | C8CIL7)
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: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: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: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: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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AG7  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3sji)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3sji
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  C8CIL7_9ENTO | C8CIL7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.4.22.28
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  C8CIL7_9ENTO | C8CIL7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        C8CIL7_9ENTO | C8CIL7: 3sj8 3sj9

(-) Related Entries Specified in the PDB File

1cqq STRUCTURE OF HRV 3C IN COMPLEX WITH AG7088
1l1n STRUCTURE OF POLIOVIRUS 3C
2zty STRUCTURE OF CVB3 3C
3sj8 STRUCTURE OF THE 3C FROM CVA16
3sj9 STRUCTURE OF THE C147A MUTANT 3C OF CVA16 IN COMPLEX WITH FAGLRQAVTQ PEPTIDE
3sjk STRUCTURE OF THE C147A MUTANT 3C FROM ENTEROVIRUS 71
3sjo STRUCTURE OF EV71 3C IN COMPLEX WITH RUPINTRIVIR (AG7088)