Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theoretical Model
collapse expand < >
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  PREDICTED 3-D MODEL OF CASPASE-6 COMPLEX WITH AC-IETD INHIBITOR
 
Authors :  R. Sattar, A. Abbasi, A. Salim
Date :  23 Aug 02  (Deposition) - 11 Sep 02  (Release) - 11 Sep 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,C
Keywords :  Caspase-6, Caspase-6 Complex With Ac-Ietd, Homology Model Of Caspase-6. (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Sattar, A. Abbasi, A. Salim
Homology Model Of Caspase-6 With Ac-Ietd Inhibitor
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASPASE-6
    ChainsA
    EC Number3.4.22.-
    FragmentRESIDUES 1-142
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
 
Molecule 2 - CASPASE-6
    ChainsB
    EC Number3.4.22.-
    FragmentRESIDUES 143-235
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
 
Molecule 3 - (ACE)IET(ASA)
    ChainsC
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ASA1Mod. Amino AcidASPARTIC ALDEHYDE

(-) Sites  (0, 0)

(no "Site" information available for 1MI9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MI9)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Arg A:9 -Arg A:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Theoretical Model (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_029242E35KCASP6_HUMANPolymorphism11574697AE2K
2UniProtVAR_016130A109TCASP6_HUMANPolymorphism5030674AA76T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Theoretical Model (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.CASP6_HUMAN43-167  1A:10-134
2CASPASE_HISPS01121 Caspase family histidine active site.CASP6_HUMAN108-122  1A:75-89
3CASPASE_CYSPS01122 Caspase family cysteine active site.CASP6_HUMAN154-165  1A:121-132

(-) Exons   (5, 6)

Theoretical Model (5, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002651641bENSE00001018825chr4:110624629-110624512118CASP6_HUMAN1-14140--
1.3ENST000002651643ENSE00000935048chr4:110619498-11061945643CASP6_HUMAN14-28150--
1.4bENST000002651644bENSE00000935047chr4:110618924-110618778147CASP6_HUMAN28-77501A:1-44
-
44
-
1.5bENST000002651645bENSE00000935046chr4:110617642-11061756677CASP6_HUMAN77-103271A:44-70
-
27
-
1.6cENST000002651646cENSE00000935045chr4:110615856-110615681176CASP6_HUMAN103-161591A:70-128
-
59
-
1.7cENST000002651647cENSE00000935044chr4:110612165-110612006160CASP6_HUMAN162-215542A:129-142
B:143-160
14
18
1.8dENST000002651648dENSE00001820381chr4:110610724-110609898827CASP6_HUMAN215-293791-
B:160-235
-
76

(-) Sequences/Alignments

Theoretical Model
   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:142
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:142
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173  
          CASP6_HUMAN    34 AEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL 175
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh........eeeeee..ee..ee........hhhhhhhhh...hhhhh...eeeeee.............. Sec.struct. author
                 SAPs(SNPs) -K-------------------------------------------------------------------------T------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------CASPASE_P20  PDB: A:10-134 UniProt: 43-167                                                                                   -------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ---------- PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: A:1-44 UniProt: 28-77       -------------------------Exon 1.6c  PDB: A:70-128 UniProt: 103-161                  Exon 1.7c      Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.5b  PDB: A:44-70    ------------------------------------------------------------------------ Transcript 1 (2)
                 1mi9 A   1 AEKYKMDHRRRGIALIFNHERFFWHLTLPERRRTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPL 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140  

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:93
                                   207       217       227       237       247       257       267       277       287   
          CASP6_HUMAN   198 YTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFP 290
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..............eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7c         --------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.8d  PDB: B:160-235 UniProt: 215-293 [INCOMPLETE]                      Transcript 1 (2)
                 1mi9 B 143 YTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFP 235
                                   152       162       172       182       192       202       212       222       232   

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1mi9 C 500 xIETd 504
                            |   |
                          500-ACE
                              504-ASA

   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 1MI9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MI9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1MI9)

(-) Gene Ontology  (16, 16)

Theoretical Model(hide GO term definitions)
Chain A,B   (CASP6_HUMAN | P55212)
molecular function
    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:0097153    cysteine-type endopeptidase activity involved in apoptotic process    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, and contributing to the apoptotic process.
    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:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006921    cellular component disassembly involved in execution phase of apoptosis    The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

 Visualization

(-) Interactive Views

Theoretical Model
  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
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ASA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1mi9)
 
  Cis Peptide Bonds
    Arg A:9 - Arg A:10   [ 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
  1mi9
    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
  CASP6_HUMAN | P55212
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.22.-
    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
  CASP6_HUMAN | P55212
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CASP6_HUMAN | P552122wdp 3k7e 3nkf 3nr2 3od5 3p45 3p4u 3qnw 3s70 3s8e 3v6l 3v6m 4ejf 4fxo 4hva 4iyr 4n5d 4n6g 4n7j 4n7m 4nbk 4nbl 4nbn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MI9)