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

(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE PROTEASE/AMIDASE FROM CLOSTRIDIUM ACETOBUTYLICUM ATCC 824
 
Authors :  Y. Patskovsky, R. Toro, J. Freeman, M. Iizuka, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  06 Apr 10  (Deposition) - 21 Apr 10  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amidotranferase-Like, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomix Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Patskovsky, R. Toro, J. Freeman, M. Iizuka, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Probable Protease/Amidase From Clostridium Acetobutylicum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTRACELLULAR PROTEASE/AMIDASE RELATED ENZYME (THIJ FAMILY)
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCA_C2826
    Organism ScientificCLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid1488
    SynonymPROBABLE PROTEASE/AMIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3MGK)

(-) Sites  (0, 0)

(no "Site" information available for 3MGK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MGK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MGK)

(-) 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:199
 aligned with Q97FB4_CLOAB | Q97FB4 from UniProtKB/TrEMBL  Length:201

    Alignment length:199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         
         Q97FB4_CLOAB     2 SYRIDVLLFNKFETLDVFGPVEIFGNLQDDFELNFISSDGGLVESSQKVRVETSLYTRDENIEKILFVPGGSGTREKVNDDNFINFIGNMVKESKYIISVCTGSALLSKAGILNGKRATTNKRSFKWVTEQNEDVLWVKEARWVKDGNIYTSSGVSAGIDMTLGFIEDLIGKEKALEISRSIEYFWNEDSNYDPFSKIY 200
               SCOP domains d3mgka_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhh.....eeeeee....eeee.....eeee.........eeeeee...hhhhhhh.hhhhhhhhhhhhhhh.eeee..hhhhhhhhh......ee.....hhhhhhh.....ee.....eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mgk A   2 SYRIDVLLFNKFETLDVFGPVEIFGNLQDDFELNFISSDGGLVESSQKVRVETSLYTRDENIEKILFVPGGSGTREKVNDDNFINFIGNMVKESKYIISVCTGSALLSKAGILNGKRATTNKRSFKWVTEQNEDVLWVKEARWVKDGNIYTSSGVSAGIDMTLGFIEDLIGKEKALEISRSIEYFWNEDSNYDPFSKIY 200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with Q97FB4_CLOAB | Q97FB4 from UniProtKB/TrEMBL  Length:201

    Alignment length:201
                             1                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 
         Q97FB4_CLOAB     - -MSYRIDVLLFNKFETLDVFGPVEIFGNLQDDFELNFISSDGGLVESSQKVRVETSLYTRDENIEKILFVPGGSGTREKVNDDNFINFIGNMVKESKYIISVCTGSALLSKAGILNGKRATTNKRSFKWVTEQNEDVLWVKEARWVKDGNIYTSSGVSAGIDMTLGFIEDLIGKEKALEISRSIEYFWNEDSNYDPFSKIY 200
               SCOP domains d3mgkb_ B: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------DUF4066-3mgkB01 B:8-168                                                                                                                                          -------------------------------- Pfam domains (1)
           Pfam domains (2) --------DUF4066-3mgkB02 B:8-168                                                                                                                                          -------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhh.....eeeeee....eeee.....eeee.........eeeeee....hhhhhh.hhhhhhhhhhhhhh..eeee..hhhhhhhhh......ee.....hhhhhhh.....ee.....eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mgk B   0 SLSYRIDVLLFNKFETLDVFGPVEIFGNLQDDFELNFISSDGGLVESSQKVRVETSLYTRDENIEKILFVPGGSGTREKVNDDNFINFIGNMVKESKYIISVCTGSALLSKAGILNGKRATTNKRSFKWVTEQNEDVLWVKEARWVKDGNIYTSSGVSAGIDMTLGFIEDLIGKEKALEISRSIEYFWNEDSNYDPFSKIY 200
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q97FB4_CLOAB | Q97FB4)
molecular function
    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.

 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
(no "Ligands, Modified Residues, Ions" information available for 3mgk)
 
  Sites
(no "Sites" information available for 3mgk)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mgk)
 

(-) 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
  3mgk
    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
  Q97FB4_CLOAB | Q97FB4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q97FB4_CLOAB | Q97FB4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3MGK)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MGK)