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(-) Description

Title :  3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 98
 
Authors :  J. Tan, M. Perbandt, J. R. Mesters, R. Hilgenfeld
Date :  24 Jul 11  (Deposition) - 08 Aug 12  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Michael Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Tan, S. George, Y. Kusov, M. Perbandt, S. Anemuller, J. R. Mesters, H. Norder, B. Coutard, C. Lacroix, P. Leyssen, J. Neyts, R. Hilgenfeld
3C Protease Of Enterovirus 68: Structure-Based Design Of Michael Acceptor Inhibitors And Their Broad-Spectrum Antiviral Effects Against Picornaviruses.
J. Virol. V. 87 4339 2013
PubMed-ID: 23388726  |  Reference-DOI: 10.1128/JVI.01123-12

(-) Compounds

Molecule 1 - 3C PROTEASE
    ChainsA
    EC Number3.4.22.28
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPINE-EV68
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VariantTUNER(DE3) PLACI
    Expression System VectorPOPINE
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1549-1731
    Organism ScientificHUMAN ENTEROVIRUS
    Organism Taxid42789
    Strain68

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1G861Ligand/IonN-(TERT-BUTOXYCARBONYL)-O-TERT-BUTYL-L-THREONYL-N-{(2R)-5-ETHOXY-5-OXO-1-[(3S)-2-OXOPYRROLIDIN-3-YL]PENTAN-2-YL}-L-PHENYLALANINAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1G862Ligand/IonN-(TERT-BUTOXYCARBONYL)-O-TERT-BUTYL-L-THREONYL-N-{(2R)-5-ETHOXY-5-OXO-1-[(3S)-2-OXOPYRROLIDIN-3-YL]PENTAN-2-YL}-L-PHENYLALANINAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:25 , PRO A:38 , HIS A:40 , ALA A:41 , GLU A:71 , LEU A:125 , ASN A:126 , GLY A:128 , THR A:142 , ARG A:143 , ALA A:144 , GLY A:145 , CYS A:147 , HIS A:161 , VAL A:162 , GLY A:163 , GLY A:164 , HOH A:2106 , HOH A:2107BINDING SITE FOR RESIDUE G86 A1190

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ZVG)

(-) 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:189
 aligned with A1E4A3_9ENTO | A1E4A3 from UniProtKB/TrEMBL  Length:2188

    Alignment length:189
                                  1558      1568      1578      1588      1598      1608      1618      1628      1638      1648      1658      1668      1678      1688      1698      1708      1718      1728         
        A1E4A3_9ENTO   1549 GPGFDFAQAIMKKNTVVARTEKGEFTMLGVHDRVAVIPTHASVGETIYINDVETKVLDACALRDLTDTNLEITIVKLDRNQKFRDIRHFLPRYEDDYNDAVLSVHTSKFPNMYIPVGQVTNYGFLNLGGTPTHRILMYNFPTRAGQCGGVVTTTGKVIGIHVGGNGAQGFAAMLLHSYFTDTQGEIVSN 1737
               SCOP domains d3zvga_ A: automated matches                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhheeeeee..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
                3zvg A    1 GPGFDFAQAIMKKNTVVARTEKGEFTMLGVHDRVAVIPTHASVGETIYINDVETKVLDACALRDLTDTNLEITIVKLDRNQKFRDIRHFLPRYEDDYNDAVLSVHTSKFPNMYIPVGQVTNYGFLNLGGTPTHRILMYNFPTRAGQCGGVVTTTGKVIGIHVGGNGAQGFAAMLLHSYFTDTQKHHHHH  189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         

   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 Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)
Chain A   (A1E4A3_9ENTO | A1E4A3)
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: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:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
    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: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.
biological process
    GO:0018144    RNA-protein covalent cross-linking    The formation of a covalent cross-link between RNA and a protein.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0039707    pore formation by virus in membrane of host cell    The aggregation, arrangement and bonding together of a set of components by a virus to form a pore complex in a membrane of a host organism.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    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: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:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0044161    host cell cytoplasmic vesicle    A vesicle formed of membrane or protein, found in the cytoplasm of a host cell.
    GO:0044162    host cell cytoplasmic vesicle membrane    The lipid bilayer surrounding a host cell cytoplasmic vesicle.
    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:0044385    integral to membrane of host cell    Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. Occurring in a host cell.
    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:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/TrEMBL
        A1E4A3_9ENTO | A1E4A33zv8 3zv9 3zva 3zvb 3zvc 3zvd 3zve 3zvf

(-) Related Entries Specified in the PDB File

3zv8 CRYSTAL STRUCTURE OF 3C PROTEASE OF ENTEROVIRUS 68
3zv9 3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 74
3zva 3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 75
3zvb 3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 81
3zvc 3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 82
3zvd 3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 83
3zve 3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 84
3zvf 3C PROTEASE OF ENTEROVIRUS 68 COMPLEXED WITH MICHAEL RECEPTOR INHIBITOR 85