Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF YOEB UNDER PEG CONDITION
 
Authors :  K. Kamada, F. Hanaoka
Date :  04 Jul 05  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Yoeb, Yefm, Toxin, Antitoxin, Addiction Modules, Rnase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Kamada, F. Hanaoka
Conformational Change In The Catalytic Site Of The Ribonuclease Yoeb Toxin By Yefm Antitoxin
Mol. Cell V. 19 497 2005
PubMed-ID: 16109374  |  Reference-DOI: 10.1016/J.MOLCEL.2005.07.004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TOXIN YOEB
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneYOEB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A     
Biological Unit 2 (1x) B    
Biological Unit 3 (1x)  C   
Biological Unit 4 (1x)   D  
Biological Unit 5 (1x)    E 
Biological Unit 6 (1x)     F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:496 , HOH A:497 , HOH A:498 , HOH A:499 , HOH A:500 , HOH A:501BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREHOH D:478 , HOH D:479 , HOH D:480 , HOH D:481 , HOH D:482 , HOH D:483BINDING SITE FOR RESIDUE MG D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A6R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A6R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A6R)

(-) Exons   (0, 0)

(no "Exon" information available for 2A6R)

(-) Sequences/Alignments

Asymmetric 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:84
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
               SCOP domains d2a6ra_ A: Toxin YoeB                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........ee.hhhhh..eeee.....eeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2a6r A  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
                                    10        20        30        40        50        60        70        80    

Chain B from PDB  Type:PROTEIN  Length:84
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
               SCOP domains d2a6rb_ B: Toxin YoeB                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhh..eeee.....eeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2a6r B  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
                                    10        20        30        40        50        60        70        80    

Chain C from PDB  Type:PROTEIN  Length:83
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:83
                                    10        20        30        40        50        60        70        80   
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYH 83
               SCOP domains d2a6rc_ C: Toxin YoeB                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee........eeee.....eeeeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  2a6r C  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYH 83
                                    10        20        30        40        50        60        70        80   

Chain D from PDB  Type:PROTEIN  Length:84
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
               SCOP domains d2a6rd_ D: Toxin YoeB                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhh..eeee.....eeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2a6r D  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
                                    10        20        30        40        50        60        70        80    

Chain E from PDB  Type:PROTEIN  Length:84
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
               SCOP domains d2a6re_ E: Toxin YoeB                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee........eeeeee..eeeeeee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2a6r E  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
                                    10        20        30        40        50        60        70        80    

Chain F from PDB  Type:PROTEIN  Length:84
 aligned with YOEB_ECOLI | P69348 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            YOEB_ECOLI    1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
               SCOP domains d2a6rf_ F: Toxin YoeB                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ee.hhhhh..eeeeee..eeeeeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2a6r F  1 MKLIWSEESWDDYLYWQETDKRIVKKINELIKDTRRTPFEGKGKPEPLKHNLSGFWSRRITEEHRLVYAVTDDSLLIAACRYHY 84
                                    10        20        30        40        50        60        70        80    

   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, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A6R)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (YOEB_ECOLI | P69348)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    GO:0016892    endoribonuclease activity, producing 3'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 3'-phosphomonoesters.
    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.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0098795    mRNA cleavage involved in gene silencing    Cleavage of an mRNA occurring as part of the mechanism of gene silencing.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0045947    negative regulation of translational initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0044010    single-species biofilm formation    A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 Visualization

(-) Interactive Views

Asymmetric 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a6r)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ Jena3D ]

(-) 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
  2a6r
    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
  YOEB_ECOLI | P69348
    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
  YOEB_ECOLI | P69348
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        YOEB_ECOLI | P693482a6q 2a6s 4v8x

(-) Related Entries Specified in the PDB File

2a6q YEFM-YOEB COMPLEX
2a6s YOEB UNDER ISOPROPANOL CONDITION