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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MOLECULAR MODEL OF THE MATURE HUMAN CATHEPSIN F
 
Authors :  A. Fengler, W. Brandt, E. Mehler, D. Bromme
Date :  12 Oct 99  (Deposition) - 28 Jun 00  (Release) - 26 Sep 01  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Thiol Protease, Cathepsin F, Papain-Like Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Fengler, W. Brandt
Development And Validation Of Homology Models Of Human Cathepsins K, S, H, And F.
Adv. Exp. Med. Biol. V. 477 255 2000
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATHEPSIN F
    ChainsA
    OrganSMOOTH MUSCLE AND BRAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Other DetailsTHIOL PROTEASE

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1D5U)

(-) Sites  (0, 0)

(no "Site" information available for 1D5U)

(-) SS Bonds  (3, 3)

Theoretical Model
No.Residues
1A:22 -A:63
2A:56 -A:96
3A:154 -A:202

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D5U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Theoretical Model (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070160Q321RCATF_HUMANDisease (CLN13)397514731AQ51R
2UniProtVAR_070161G458ACATF_HUMANDisease (CLN13)397514732AG188A
3UniProtVAR_070162S480LCATF_HUMANDisease (CLN13)397514733AS210L

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

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATF_HUMAN289-300  1A:19-30
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATF_HUMAN429-439  1A:159-169

(-) Exons   (8, 8)

Theoretical Model (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003103252ENSE00001188380chr11:66336067-66335745323CATF_HUMAN1-71710--
1.3ENST000003103253ENSE00001188376chr11:66335553-6633545599CATF_HUMAN72-104330--
1.4cENST000003103254cENSE00001188372chr11:66335133-66334915219CATF_HUMAN105-177730--
1.5aENST000003103255aENSE00001233025chr11:66334792-6633471776CATF_HUMAN178-203260--
1.6bENST000003103256bENSE00001188359chr11:66333875-66333762114CATF_HUMAN203-241390--
1.7aENST000003103257aENSE00001188356chr11:66333638-66333493146CATF_HUMAN241-289491A:1-1919
1.8aENST000003103258aENSE00001188351chr11:66333398-6633330297CATF_HUMAN290-322331A:20-5233
1.8cENST000003103258cENSE00001188349chr11:66333222-6633314281CATF_HUMAN322-349281A:52-7928
1.9aENST000003103259aENSE00001188347chr11:66332477-66332358120CATF_HUMAN349-389411A:79-11941
1.9cENST000003103259cENSE00001188342chr11:66332277-6633221365CATF_HUMAN389-410221A:119-14022
1.10bENST0000031032510bENSE00001233018chr11:66332119-6633202991CATF_HUMAN411-441311A:141-17131
1.10eENST0000031032510eENSE00001188333chr11:66331617-6633155959CATF_HUMAN441-460201A:171-19020
1.11bENST0000031032511bENSE00002162432chr11:66331478-66330934545CATF_HUMAN461-484241A:191-21424

(-) 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:214
 aligned with CATF_HUMAN | Q9UBX1 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:214
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480    
           CATF_HUMAN   271 APPEWDWRSKGAVTKVKDQGMCGSCWAFSVTGNVEGQWFLNQGTLLSLSEQELLDCDKMDKACMGGLPSNAYSAIKNLGGLETEDDYSYQGHMQSCNFSAEKAKVYINDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPLRPLCSPWLIDHAVLLVGYGNRSDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAVVD 484
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...................hhhhh...eeeeee...hhhhhhhhhhhh..eeeee..........................eeeeeeeeee....eeeeee...........eeeee...hhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------A---------------------L---- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA--------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7a          Exon 1.8a  PDB: A:20-52          --------------------------Exon 1.9a  PDB: A:79-119 UniProt: 349-389---------------------Exon 1.10b  PDB: A:141-171     -------------------Exon 1.11b               Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.8c  PDB: A:52-79     ---------------------------------------Exon 1.9c             ------------------------------Exon 1.10e          ------------------------ Transcript 1 (2)
                 1d5u A   1 APPEWDWRSKGAVTKVKDQGMCGSCWAFSVTGNVEGQWFLNQGTLLSLSEQELLDCDKMDKACMGGLPSNAYSAIKNLGGLETEDDYSYQGHMQSCNFSAEKAKVYINDSVELSQNEQKLAAWLAKRGPISVAINAFGMQFYRHGISRPLRPLCSPWLIDHAVLLVGYGNRSDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAVVD 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    

   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 1D5U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1D5U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D5U)

(-) Gene Ontology  (12, 12)

Theoretical Model(hide GO term definitions)
Chain A   (CATF_HUMAN | Q9UBX1)
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: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: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.
biological process
    GO:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CATF_HUMAN | Q9UBX11m6d

(-) Related Entries Specified in the PDB File

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