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 :  HCMV PROTEASE DIMER-INTERFACE MUTANT, S225Y COMPLEXED TO INHIBITOR BILC 408
 
Authors :  R. Batra, R. Khayat, L. Tong
Date :  03 Aug 01  (Deposition) - 12 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Herpesvirus, Cytomegalovirus, Serine Protease, Dimerization, Enzyme Activity Regulation, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Batra, R. Khayat, L. Tong
Molecular Mechanism For Dimerization To Regulate The Catalytic Activity Of Human Cytomegalovirus Protease.
Nat. Struct. Biol. V. 8 810 2001
PubMed-ID: 11524687  |  Reference-DOI: 10.1038/NSB0901-810

(-) Compounds

Molecule 1 - ASSEMBLIN
    Chains: A, B
    EC Number: 3.4.21.97
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: HUMAN CYTOMEGALOVIRUS
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 10359
    Synonym: PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
10FP2Ligand/IonN-(6-AMINOHEXANOYL)-3-METHYL-L-VALYL-3-METHYL-L-VALYL-N~1~-[(2S,3S)-3-HYDROXY-4-OXO-4-{[(1R)-1-PHENYLPROPYL]AMINO}BUTAN-2-YL]-N~4~,N~4~-DIMETHYL-L-ASPARTAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:1031 , ASN A:1062 , HIS A:1063 , SER A:1132 , LEU A:1133 , SER A:1134 , SER A:1135 , CYS A:1161 , VAL A:1163 , GLY A:1164 , ARG A:1165 , ARG A:1166 , ILE A:1231BINDING SITE FOR RESIDUE 0FP A 261
2AC2SOFTWAREGLU B:1331 , ASN B:1362 , HIS B:1363 , SER B:1432 , LEU B:1433 , SER B:1434 , SER B:1435 , ARG B:1436 , LYS B:1456 , VAL B:1463 , GLY B:1464 , ARG B:1465 , ILE B:1531BINDING SITE FOR RESIDUE 0FP B 561

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JQ7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JQ7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JQ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JQ7)

(-) Exons   (0, 0)

(no "Exon" information available for 1JQ7)

(-) 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:210
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:250
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256
          SCAF_HCMVA      7 QSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  256
               SCOP domains d1jq7a_ A: Human cytomegalovirus prot          ease                                                                                                                                                                                                        SCOP domains
               CATH domains 1jq7A00 A:1007-1256 Serine Protease,           Human Cytomegalovirus Protease; Chain A                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee...............hhhhhhhhh----------....eeee......eeee..ee.......eeeeee...hhhhhhhhhhh...............hhhhhhhhhhh.eeeee.------------------...eeeee..........eee.hhhhhhh......hhhhhhhh...------------.....hhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jq7 A 1007 QSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWL----------SVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSS------------------PFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQW------------DPFRSDSYGLLGNYVDALYIRERLPKLRYDKQLVGVTERESYVKA 1256
                                  1016      1026      1036      |  -      1056      1066      1076      1086      1096      1106      1116      1126        |-         -      1156      1166      1176      1186      1196  |      -     |1216      1226      1236      1246      1256
                                                             1043       1054                                                                             1135               1154                                         1199         1212                                            


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with SCAF_HCMVA | P16753 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:250
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256
          SCAF_HCMVA      7 QSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWLHAQGQGQPSLSVALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCDDVEAATSLSGSETTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGSTAVDASGDPFRSDSYGLLGNSVDALYIRERLPKLRYDKQLVGVTERESYVKA  256
               SCOP domains d1jq7b_ B: Human cytomegalovirus prot            ease                                                                                                                                                                                                      SCOP domains
               CATH domains 1jq7B00 B:1307-1556 Serine Protease,             Human Cytomegalovirus Protease; Chain A                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee......hhhhh.hhhhhhhhh------------..eeee......eeeeeeeeee...eeeeeeee...hhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhh.eeeee.....------------.....eeeee..........eee.hhhhhhh.....hhhhhhhhhhhhh---------.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jq7 B 1307 QSQAVAPVYVGGFLARYDQSPDEAELLLPRDVVEHWL------------ALPLNINHDDTAVVGHVAAMQSVRDGLFCLGCVTSPRFLEIVRRASEKSELVSRGPVSPLQPDKVVEFLSGSYAGLSLSSRRCD------------TTPFKHVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQ---------SGDPFRSDSYGLLGNYVDALYIRERLPKLRYDKQLVGVTERESYVKA 1556
                                  1316      1326      1336      |  -      1356      1366      1376      1386      1396      1406      1416      1426      1436  |      -     |1456      1466      1476      1486      1496   |     -   |  1516      1526      1536      1546      1556
                                                             1343         1356                                                                               1439         1452                                            1500      1510
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JQ7)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SCAF_HCMVA | P16753)
molecular function
    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: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: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).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

 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
    0FP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1jq7)
 

(-) 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
  1jq7
    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
  SCAF_HCMVA | P16753
    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)
  3.4.21.97
    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
  SCAF_HCMVA | P16753
    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
        SCAF_HCMVA | P16753: 1cmv 1id4 1iec 1ied 1ief 1ieg 1jq6 1lay 1njt 1nju 1nkk 1nkm 1wpo 2wpo

(-) Related Entries Specified in the PDB File

1jq6 HUMAN CYTOMEGALOVIRUS PROTEASE MUTANT, S225Y
1wpo STRUCTURE OF HUMAN CYTOMEGALOVIRUS PROTEASE
2wpo HUMAN CYTOMEGALOVIRUS PROTEASE COMPLEXED TO PEPTIDOMIMETIC INHIBITOR BILC821