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 :  MESOTRYPSIN IN COMPLEX WITH CLEAVED AMYLOID PRECURSOR LIKE PROTEIN 2 INHIBITOR (APLP2)
 
Authors :  O. Kayode, R. Wang, D. Pendlebury, A. Soares, E. S. Radisky
Date :  13 Apr 16  (Deposition) - 09 Nov 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,X,Y
Keywords :  Inhibitor Protease Serine, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Kayode, R. Wang, D. F. Pendlebury, I. Cohen, R. D. Henin, A. Hockla, A. S. Soares, N. Papo, T. R. Caulfield, E. S. Radisky
An Acrobatic Substrate Metamorphosis Reveals A Requirement For Substrate Conformational Dynamics In Trypsin Proteolysis.
J. Biol. Chem. V. 291 26304 2016
PubMed-ID: 27810896  |  Reference-DOI: 10.1074/JBC.M116.758417

(-) Compounds

Molecule 1 - PRSS3 PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRAP-T7-WTHU3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GenePRSS3
    MutationYES
    OrganPANCREAS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - AMYLOID-LIKE PROTEIN 2
    ChainsX
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICZA
    Expression System Taxid4922
    GeneAPLP2, APPL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPLP-2,APPH,AMYLOID PROTEIN HOMOLOG,CDEI BOX-BINDING PROTEIN,CDEBP
 
Molecule 3 - AMYLOID-LIKE PROTEIN 2
    ChainsY
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS
    Expression System PlasmidPPICZA
    Expression System Taxid4922
    GeneAPLP2, APPL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPLP-2,APPH,AMYLOID PROTEIN HOMOLOG,CDEI BOX-BINDING PROTEIN,CDEBP

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AXY

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , ASN A:72 , VAL A:75 , GLU A:77 , GLU A:80 , HOH A:463binding site for residue CA A 301
2AC2SOFTWAREHIS A:217 , GLY A:219 , GLY X:12 , PRO X:13 , ARG Y:42 , ASN Y:43 , ASN Y:44 , HOH Y:202 , HOH Y:218binding site for residue SO4 Y 101

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:136 -A:201
4A:168 -A:182
5A:191 -A:220
6X:5 -Y:55
7X:14 -Y:38
8Y:30 -Y:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JBT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JBT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JBT)

(-) Exons   (0, 0)

(no "Exon" information available for 5JBT)

(-) 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:224
                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee...eeeeeeeee..eeeehhhhh....eeee............eeeeeeeeee.............eeeee........................eeeeee...............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee..........eeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jbt A   16 IVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEGNEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTAPPAAGTECLISGWGNTLSFGADYPDELKCLDAPVLTQAECKASYPGKITNSMFCVGFLEGGKDSCQRDAGGPVVCNGQLQGVVSWGHGCAWKNRPGVYTKVYNYVDWIKDTIAANS  246
                                    25        37        47        57        67|       78        88        98       108       118      |129||     140       150       160       170       180   |   188       198     ||212    || 222       232       242    
                                             34|                            67|                                                     125|  ||                                                184A 188A              204|     217| |                          
                                              37                             69                                                      127  ||                                                                        209      219 |                          
                                                                                                                                        130|                                                                                  221A                          
                                                                                                                                         132                                                                                                                

Chain X from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                5jbt X    2 KAVCSQEAMTGPCR   15
                                    11    

Chain Y from PDB  Type:PROTEIN  Length:38
                                                                       
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeee.....hhhhh...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                5jbt Y   18 MPRWYFDLSKGKCVRFIYGGCGGNRNNFESEDYCMAVC   55
                                    27        37        47        

   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 5JBT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JBT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JBT)

(-) Gene Ontology  (30, 34)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5jbt)
 

(-) 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
  5jbt
    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
  APLP2_HUMAN | Q06481
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  Q8N2U3_HUMAN | Q8N2U3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TRY3_HUMAN | P35030
    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
  APLP2_HUMAN | Q06481
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q8N2U3_HUMAN | Q8N2U3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TRY3_HUMAN | P35030
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q8N2U3_HUMAN | Q8N2U33l3t 3p92 3p95 4dg4
        TRY3_HUMAN | P350301h4w 2r9p 3l33 3l3t 3p92 3p95 4dg4 4u30 4u32 5c67 5tp0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JBT)