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(-) Description

Title :  STRUCTURE OF CATHEPSIN B1 FROM SCHISTOSOMA MANSONI IN COMPLEX WITH K11017 INHIBITOR
 
Authors :  P. Rezacova, A. Jilkova, J. Brynda, M. Horn, M. Mares
Date :  18 May 11  (Deposition) - 10 Aug 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidase, Digestive Tract, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jilkova, P. Rezacova, M. Lepsik, M. Horn, J. Vachova, J. Fanfrlik, J. Brynda, J. H. Mckerrow, C. R. Caffrey, M. Mares
Structural Basis For Inhibition Of Cathepsin B Drug Target From The Human Blood Fluke, Schistosoma Mansoni.
J. Biol. Chem. V. 286 35770 2011
PubMed-ID: 21832058  |  Reference-DOI: 10.1074/JBC.M111.271304

(-) Compounds

Molecule 1 - CATHEPSIN B-LIKE PEPTIDASE (C01 FAMILY)
    Chains: A
    EC Number: 3.4.22.1
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: X33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 87-340
    Gene: CB1.1, SMP_103610
    Mutation: YES
    Organism Common: BLOOD FLUKE
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183
    Synonym: CATHEPSIN B1 ISOTYPE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2C1P1Ligand/IonN~2~-(MORPHOLIN-4-YLCARBONYL)-N-[(3S)-1-PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]-L-LEUCINAMIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:94 , GLY A:98 , CYS A:100 , TRP A:101 , CYS A:141 , GLU A:142 , GLY A:143 , GLY A:144 , LEU A:146 , ILE A:193 , VAL A:247 , GLY A:269 , HIS A:270 , TRP A:292 , GLU A:316 , HOH A:469 , HOH A:600BINDING SITE FOR RESIDUE C1P A 1
2AC2SOFTWAREGLN A:121 , LYS A:215 , HIS A:216 , ARG A:217 , HOH A:349 , HOH A:544 , HOH A:578 , HOH A:684BINDING SITE FOR RESIDUE ACT A 324
3AC3SOFTWAREHOH A:24 , GLU A:179 , HIS A:180 , HIS A:181 , PRO A:188 , GLY A:190 , HOH A:354 , HOH A:793BINDING SITE FOR RESIDUE ACT A 2

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:85 -A:114
2A:97 -A:141
3A:133 -A:199
4A:134 -A:137
5A:170 -A:203
6A:178 -A:189

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S3Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3S3Q)

(-) 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:254
 aligned with Q8MNY2_SCHMA | Q8MNY2 from UniProtKB/TrEMBL  Length:340

    Alignment length:254
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    
         Q8MNY2_SCHMA    87 VEIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHTGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKTPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 340
               SCOP domains d3s3qa_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eehhhhh................hhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhh.hhhhhhhhhhhh.....................................................hhhhhh....eeee...hhhhhhhhhhhhh.eeeeeeee.hhhhh...ee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s3q A  70 VEIPSSFDSRKKWPRCKSIATIRDQSRCGSCWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S3Q)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8MNY2_SCHMA | Q8MNY2)
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: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.
    GO:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
cellular component
    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: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/TrEMBL
        Q8MNY2_SCHMA | Q8MNY2: 3qsd 3s3r 4i04 4i05 4i07

(-) Related Entries Specified in the PDB File

3qsd 3s3r