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 :  STRUCTURE OF SARS-3CL PROTEASE COMPLEX WITH A PHENYLBENZOYL (R,S)-N-DECALIN TYPE INHIBITOR
 
Authors :  K. Akaji, K. Teruya, Y. Shimamoto, A. Sanjho, E. Yamashita, A. Nakagawa
Date :  15 Nov 14  (Deposition) - 18 Feb 15  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrase Proteinase Converting, Designed Inhibitor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shimamoto, Y. Hattori, K. Kobayashi, K. Teruya, A. Sanjoh, A. Nakagawa, E. Yamashita, K. Akaji
Fused-Ring Structure Of Decahydroisoquinolin As A Novel Scaffold For Sars 3Cl Protease Inhibitors.
Bioorg. Med. Chem. V. 23 876 2015
PubMed-ID: 25614110  |  Reference-DOI: 10.1016/J.BMC.2014.12.028

(-) Compounds

Molecule 1 - 3C-LIKE PROTEINASE
    Chains: A
    EC Number: 3.4.22.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-3CL-R188I
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: REP, 1A-1B
    Organism Common: SARS-COV
    Organism Scientific: SARS CORONAVIRUS
    Organism Taxid: 227859
    Synonym: 3CL-PRO, 3CLP, NSP5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
13X51Ligand/Ion(2S)-2-({[(3R,4AS,8AR)-2-(BIPHENYL-4-YLCARBONYL)DECAHYDROISOQUINOLIN-3-YL]METHYL}AMINO)-3-(1H-IMIDAZOL-5-YL)PROPANAL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:41 , MET A:49 , PHE A:140 , LEU A:141 , ASN A:142 , GLY A:143 , CYS A:145 , HIS A:163 , HIS A:164 , MET A:165 , GLU A:166 , ASP A:187 , ILE A:188 , GLN A:189 , HOH A:520 , HOH A:524 , HOH A:526 , HOH A:580binding site for residue 3X5 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WY3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WY3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WY3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WY3)

(-) Exons   (0, 0)

(no "Exon" information available for 4WY3)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh.eeeeee..eeeeeeee..eeeee.hhhh..hhhhh.hhhhhhhh.hhh.eeeee..eee.eeeeeee..eeeeee.........eee.......eeeeeeee..eeeeeeeee..................eeeeee..eeeeeeeeeee.....eeee........................hhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh................hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wy3 A   1 SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLNPNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDIQTAQAAGTDTTITLNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSGVTFQ 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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)

(no "SCOP Domain" information available for 4WY3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WY3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WY3)

(-) Gene Ontology  (64, 64)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    3X5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4wy3)
 

(-) 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
  4wy3
    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
  R1AB_CVHSA | P0C6X7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.22.-
    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
  R1AB_CVHSA | P0C6X7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        R1AB_CVHSA | P0C6X7: 1o5s 1p76 1p9t 1pa5 1puk 1q1x 1q2w 1qz8 1sxf 1uj1 1uk2 1uk3 1uk4 1uw7 1wof 1ysy 1z1i 1z1j 2a5a 2a5i 2a5k 2acf 2ahm 2aj5 2alv 2amd 2amq 2bx3 2bx4 2c3s 2d2d 2duc 2fav 2fe8 2fyg 2g1f 2g9t 2ga6 2gdt 2gri 2gt7 2gt8 2gtb 2gx4 2gz7 2gz8 2gz9 2h2z 2h85 2hob 2hsx 2idy 2jzd 2jze 2jzf 2k87 2op9 2ozk 2pwx 2q6g 2qc2 2qcy 2qiq 2rhb 2rnk 2v6n 2vj1 2xyq 2xyr 2xyv 2z3c 2z3d 2z3e 2z94 2z9g 2z9j 2z9k 2z9l 3d62 3e9s 3ebn 3r24 4tww 4twy 4zuh 5b6o 5c5n 5c5o 5c8s 5c8t 5c8u 5e6j 5f22 5tl6 5tl7

(-) Related Entries Specified in the PDB File

3atw