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 PUTATIVE CTP PYROPHOSPHOHYDROLASE FROM BACTEROIDES FRAGILIS
 
Authors :  Y. Patskovsky, R. Romero, M. Gilmore, J. Do, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  01 Apr 09  (Deposition) - 14 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Hydrolase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Romero, M. Gilmore, J. Do, S. Wasserman, J. M. Sauder S. K. Burley, S. C. Almo
Crystal Structure Of Ctp Pyrophosphohydrolase From Bacteroides Fragilis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE CTP PYROPHOSPHOHYDROLASE
    Atcc: 25285
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BF2916
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 272559
    Strain: NCTC 9343

 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 3GWY)

(-) Sites  (0, 0)

(no "Site" information available for 3GWY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GWY)

(-) 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:121
 aligned with Q5LBB1_BACFN | Q5LBB1 from UniProtKB/TrEMBL  Length:130

    Alignment length:130
                             1                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129
         Q5LBB1_BACFN     - -MKSIEVVAAVIRLGEKYLCVQRGQTKFSYTSFRYEFPGGKVEEGESLQEALQREIMEEMDYVIEVGEKLLTVHHTYPDFEITMHAFLCHPVGQRYVLKEHIAAQWLSTREMAILDWAEADKPIVRKISE 129
               SCOP domains d3gwya_ A: automated ma         tches                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..eeeeee.---------..ee..eee.....hhhhhhhhhhhhhhh..eeeeeeeeeee.......eeeeeeeeee...........eeeeehhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwy A   0 SLKSIEVVAAVIRLGEKYLCVQR---------FRYEFPGGKVEEGESLQEALQREIMEEMDYVIEVGEKLLTVHHTYPDFEITMHAFLCHPVGQRYVLKEHIAAQWLSTREMAILDWAEADKPIVRKISE 129
                                     9        19  |      -  |     39        49        59        69        79        89        99       109       119       129
                                                 22        32                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with Q5LBB1_BACFN | Q5LBB1 from UniProtKB/TrEMBL  Length:130

    Alignment length:133
                             1                                                                                                                              130  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129|  
         Q5LBB1_BACFN     - -MKSIEVVAAVIRLGEKYLCVQRGQTKFSYTSFRYEFPGGKVEEGESLQEALQREIMEEMDYVIEVGEKLLTVHHTYPDFEITMHAFLCHPVGQRYVLKEHIAAQWLSTREMAILDWAEADKPIVRKISEQ--   -
               SCOP domains d3gwyb_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee..eeeeeee...............eee.....hhhhhhhhhhhhhhh..eeeeeeeeeeeee....eeeeeeeeeee..........eeeeeehhhhhh.......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwy B   0 SLKSIEVVAAVIRLGEKYLCVQRGQTKFSYTSFRYEFPGGKVEEGESLQEALQREIMEEMDYVIEVGEKLLTVHHTYPDFEITMHAFLCHPVGQRYVLKEHIAAQWLSTREMAILDWAEADKPIVRKISEQEG 132
                                     9        19        29        39        49        59        69        79        89        99       109       119       129
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5LBB1_BACFN | Q5LBB1)
molecular function
    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.

 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 3gwy)
 
  Sites
(no "Sites" information available for 3gwy)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3gwy)
 

(-) 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 ](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
  3gwy
    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
  Q5LBB1_BACFN | Q5LBB1
    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)
  (no 'Enzyme Classificator' available)
    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
  Q5LBB1_BACFN | Q5LBB1
    Protein Disorder Prediction: DisEMBL | 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 3GWY)

(-) Related Entries Specified in the PDB File

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