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 :  STRUCTURE OF INTERMEDIATE PROCESSING FORM OF CATHEPSIN B1 FROM SCHISTOSOMA MANSONI
 
Authors :  P. Rezacova, A. Jilkova, J. Brynda, M. Horn, M. Mares
Date :  16 Nov 12  (Deposition) - 05 Feb 14  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidase, Digestive Tract, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jilkova, M. Horn, P. Rezacova, L. Maresova, P. Fajtova, J. Brynda, J. Vondrasek, J. H. Mckerrow, C. R. Caffrey, M. Mares
Activation Route Of The Schistosoma Mansoni Cathepsin B1 Drug Target: Structural Map With A Glycosaminoglycan Switch
Structure V. 22 1786 2014
PubMed-ID: 25456815  |  Reference-DOI: 10.1016/J.STR.2014.09.015

(-) 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 Common: YEAST
    Expression System Plasmid: PPICZALPHA
    Expression System Strain: X33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 56-340
    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, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
2NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:92 , SER A:163 , HOH A:508 , HOH A:516 , HOH A:517BINDING SITE FOR RESIDUE NA A 401

(-) SS Bonds  (6, 6)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I05)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I05)

(-) Exons   (0, 0)

(no "Exon" information available for 4I05)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh.ee............eehhhhh..hhhhhh........hhhhhhhhhhhhhhhhhh.........hhhhhhhhh....hhhhh.hhhhhhhhhhhh.....................................................hhhhhh....eeeee..hhhhhhhhhhhhh.eeeeeeee.hhhhh...ee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i05 A  47 GARREEPDLRRTRRPTVDHNDWNVEIPSSFDSRKKWPRCKSIATIRDQSRCGScWAFGAVEAMSDRSCIQSGGKQNVELSAVDLLSCCESCGLGCEGGILGPAWDYWVKEGIVTGSSKENHAGCEPYPFPKCEHHTKGKYPPCGSKIYKTPRCKQTCQKKYKTPYTQDKHRGKSSYNVKNDEKAIQKEIMKYGPVEAGFTVYEDFLNYKSGIYKHITGETLGGHAIRIIGWGVENKAPYWLIANSWNEDWGENGYFRIVRGRDECSIESEVTAGRIN 323
                                    56        66        76        86        96   |   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       
                                                                               100-CSO
   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 4I05)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I05)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I05)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4i05)
 

(-) 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
  4i05
    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
  Q8MNY2_SCHMA | Q8MNY2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.4.22.1
    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
  Q8MNY2_SCHMA | Q8MNY2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8MNY2_SCHMA | Q8MNY2: 3qsd 3s3q 3s3r 4i04 4i07

(-) Related Entries Specified in the PDB File

3qsd MATURE SMCB1 IN COMPLEX WITH INHIBITOR CA074
3s3q MATURE SMCB1 IN COMPLEX WITH INHIBITOR K11017
3s3r MATURE SMCB1 IN COMPLEX WITH INHIBITOR K11777
4i04 SMCB1 ZYMOGEN
4i07