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 :  1.65 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA
 
Authors :  M. Simonovic, P. G. W. Gettins, K. Volz
Date :  26 Jul 02  (Deposition) - 05 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Serpin, Crma, Apoptosis, Ice Inhibitor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Simonovic, P. G. W. Gettins, K. Volz
Crystal Structure Of Viral Serpin Crma Provides Insights Into Its Mechanism Of Cysteine Proteinase Inhibition
Protein Sci. V. 9 1423 2000
PubMed-ID: 10975564
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE PROTEINASE INHIBITOR 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-60
    Expression System StrainSG13009
    Expression System Taxid562
    FragmentRESIDUES 1-55
    GeneCRMA
    Organism ScientificCOWPOX VIRUS
    Organism Taxid10243
    SynonymCYTOKINE RESPONSE MODIFIER PROTEIN A, SERPIN 2, SERP-2, ICE INHIBITOR, HEMORRHAGE-INDUCING 38 KDA PROTEIN
 
Molecule 2 - SERINE PROTEINASE INHIBITOR 2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-60
    Expression System StrainSG13009
    Expression System Taxid562
    FragmentRESIDUES 56-300
    GeneCRMA
    MutationYES
    Organism ScientificCOWPOX VIRUS
    Organism Taxid10243
    SynonymCYTOKINE RESPONSE MODIFIER PROTEIN A, SERPIN 2, SERP-2, ICE INHIBITOR, HEMORRHAGE-INDUCING 38 KDA PROTEIN
 
Molecule 3 - SERINE PROTEINASE INHIBITOR 2
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-60
    Expression System StrainSG13009
    Expression System Taxid562
    FragmentRESIDUES 301-341
    GeneCRMA
    MutationYES
    Organism ScientificCOWPOX VIRUS
    Organism Taxid10243
    SynonymCYTOKINE RESPONSE MODIFIER PROTEIN A, SERPIN 2, SERP-2, ICE INHIBITOR, HEMORRHAGE-INDUCING 38 KDA PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , ASP A:2 , ARG A:5 , HOH A:566 , THR B:215 , ASP B:216BINDING SITE FOR RESIDUE PO4 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M93)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M93)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.SPI2_CWPXB312-322  1C:312-322

(-) Exons   (0, 0)

(no "Exon" information available for 1M93)

(-) 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:46
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:46
                                    10        20        30        40      
           SPI2_CWPXB     1 MDIFREIASSMKGENVFISPPSISSVLTILYYGANGSTAEQLSKYV  46
               SCOP domains d1m93.1 A:,B:,C:                               SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1m93 A   1 MDIFREIASSMKGENVFISPPSISSVLTILYYGANGSTAEQLSKYV  46
                                    10        20        30        40      

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:245
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     
           SPI2_CWPXB    56 DISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDCRTVDAINKCVDIFTEGKINPLLDEPLSPDTCLLAISAVYFKAKWLMPFEKEFTSDYPFYVSPTEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWCDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGLTEVFGSTGDYSNMCNSDVSVDAMIHKTYIDVNEEYTEAAAATCAL 300
               SCOP domains d1m93.1 A:,B:,C: Viral serpin crmA (cytokine response modifier protein)                                                                                                                                                                               SCOP domains
               CATH domains 1m93B01 B:56-132,B:241-283,B:294-300 Antithrombin, subunit I, domain 2       1m93B02 B:133-240,B:284-293 Alpha-1-antitrypsin, domain 1                                                   1m93B01 B:56-132,B:241-283,B:294-300       1m93B02   1m93B01 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.....hhhhhhhhh..eeee....hhhhhhhhhhhhhhh.................eeeeeeeeeeee.....hhhhheeeeeeee..eeeeeeeeee...eeeeeee......eeeeeee....eeeeeeee....hhhhhhh..hhhhhhhhhhh.eeee.eeeee.eeeeeeeehhhhhhhh........................eeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m93 B  56 DISFKSMNKVYGRYSAVFKDSFLRKIGDNFQTVDFTDSRTVDAINKSVDIFTEGKINPLLDEPLSPDTSLLAISAVYFKAKWLMPFEKEFTSDYPFYVSPTEMVDVSMMSMYGEAFNHASVKESFGNFSIIELPYVGDTSMVVILPDNIDGLESIEQNLTDTNFKKWSDSMDAMFIDVHIPKFKVTGSYNLVDALVKLGLTEVFGSTGDYSNMSNSDVSVDAMIHKTYIDVNEEYTEAAAATSAL 300
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295     

Chain C from PDB  Type:PROTEIN  Length:31
 aligned with SPI2_CWPXB | P07385 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:31
                                   318       328       338 
           SPI2_CWPXB   309 TNEFCADHPFIYVIRHVDGKILFVGRYCSPT 339
               SCOP domains d1m93.1 A:,B:,C:                SCOP domains
               CATH domains ------------------------------- CATH domains
           Pfam domains (1) Serpin-1m93C01 C:309-338      - Pfam domains (1)
           Pfam domains (2) Serpin-1m93C02 C:309-338      - Pfam domains (2)
           Pfam domains (3) Serpin-1m93C03 C:309-338      - Pfam domains (3)
         Sec.struct. author ..eee....eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ---SERPIN     ----------------- PROSITE
                 Transcript ------------------------------- Transcript
                 1m93 C 309 TNEFSADHPFIYVIRHVDGKILFVGRYSSPT 339
                                   318       328       338 

   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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (SPI2_CWPXB | P07385)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0039526    modulation by virus of host apoptotic process    Any process in which a virus modulates the frequency, rate or extent of apoptosis of infected host cells.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0039650    suppression by virus of host cysteine-type endopeptidase activity involved in apoptotic process    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host caspase activity. Caspases are cysteine-type endopeptidases which contribute to the apoptotic process.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

 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
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn B:112 - Pro B:113   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1m93
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPI2_CWPXB | P07385
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SPI2_CWPXB | P07385
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPI2_CWPXB | P073851c8o 1f0c

(-) Related Entries Specified in the PDB File

1c8o 1C8O IS THE 2.9 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA
1f0c 1F0C IS THE STRUCTURE OF THE VIRAL SERPIN CRMA