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 :  CRYSTAL STRUCTURE OF BORRELIA BURGDORFERI PUR-ALPHA
 
Authors :  A. Graebsch, S. Roche, D. Kostrewa, D. Niessing
Date :  28 May 10  (Deposition) - 06 Oct 10  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pur-Alpha, Pur Repeat, Pur Domain, Whirly Fold, Rna Binding, Dna Binding, Nucleic Acid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Graebsch, S. Roche, D. Kostrewa, J. Soding, D. Niessing
Of Bits And Bugs--On The Use Of Bioinformatics And A Bacterial Crystal Structure To Solve A Eukaryotic Repeat-Protein Structure.
Plos One V. 5 13402 2010
PubMed-ID: 20976240  |  Reference-DOI: 10.1371/JOURNAL.PONE.0013402
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PUR-ALPHA RESIDUES 8-105
    Gene: BB_0047
    Mutation: YES
    Organism Common: LYME DISEASE SPIROCHETE
    Organism Scientific: BORRELIA BURGDORFERI
    Organism Taxid: 139

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MG2Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:33 , EDO B:1 , SER B:21 , GLU B:22 , ARG B:23BINDING SITE FOR RESIDUE EDO A 1
2AC2SOFTWAREGLU A:61 , GLU A:62 , ASN A:63 , MSE A:64 , ASN A:65 , GLU A:66 , HOH A:114 , HOH A:141 , HOH A:180BINDING SITE FOR RESIDUE EDO A 106
3AC3SOFTWARETYR A:13 , SER A:14 , GLU A:15 , HOH A:183BINDING SITE FOR RESIDUE EDO A 107
4AC4SOFTWAREHOH A:2 , THR A:19 , SER A:21BINDING SITE FOR RESIDUE MG A 108
5AC5SOFTWAREEDO A:1 , ARG A:33 , LYS A:34 , HOH A:112 , HOH A:166 , ARG B:46 , PRO B:48BINDING SITE FOR RESIDUE EDO B 1
6AC6SOFTWARETHR B:19 , SER B:21 , HOH B:112BINDING SITE FOR RESIDUE MG B 106

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N8B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N8B)

(-) Exons   (0, 0)

(no "Exon" information available for 3N8B)

(-) 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:75
 aligned with O51076_BORBU | O51076 from UniProtKB/TrEMBL  Length:122

    Alignment length:75
                                    12        22        32        42        52        62        72     
          O51076_BORBU    3 ERGEVYSEKLFTESERTYFFNVKENRKGDYFLNIVESKRSPSGDFERHSIFVYEENINEFESNLLKAIAVIKQKV 77
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....eeeeeeeee.....eeeeeeeeee.....eeeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                  3n8b A  8 ERGEVYSEKmFTESERTYFmNVKENRKGDYFLNIVESKRSPSGDFERHSIFVYEENmNEFESNLLKAIAVIKQKV 82
                                    17        27        37        47        57      | 67        77     
                                    17-MSE    27-MSE                               64-MSE              


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with O51076_BORBU | O51076 from UniProtKB/TrEMBL  Length:122

    Alignment length:74
                                    15        25        35        45        55        65        75    
          O51076_BORBU    6 EVYSEKLFTESERTYFFNVKENRKGDYFLNIVESKRSPSGDFERHSIFVYEENINEFESNLLKAIAVIKQKVST 79
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --DUF3276-3n8bB01 B:13-84                                                  Pfam domains (1)
           Pfam domains (2) --DUF3276-3n8bB02 B:13-84                                                  Pfam domains (2)
         Sec.struct. author ..eeeee.....eeeeeeeee.....eeeeeeeeee.....eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                  3n8b B 11 EVYSEKmFTESERTYFmNVKENRKGDYFLNIVESKRSPSGDFERHSIFVYEENmNEFESNLLKAIAVIKQKVST 84
                                  | 20      | 30        40        50        60   |    70        80    
                                 17-MSE    27-MSE                               64-MSE
   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 3N8B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N8B)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF3276] (2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3N8B)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3n8b)
 

(-) 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
  3n8b
    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
  O51076_BORBU | O51076
    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
  O51076_BORBU | O51076
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O51076_BORBU | O51076: 3nm7

(-) Related Entries Specified in the PDB File

3k44 CRYSTAL STRUCTURE OF DROSOPHILA MELANOGASTER PUR-ALPHA