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 A MEMBER OF THE VAPBC FAMILY OF TOXIN-ANTITOXIN SYSTEMS, VAPBC-5, FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  L. Miallau, D. Cascio, D. Eisenberg, Integrated Center For Structu Function Innovation (Isfi), Tb Structural Genomics Consortiu
Date :  02 Jun 08  (Deposition) - 15 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Toxin Antitoxin Complex, Vapbc, Mycobacterium Tuberculosis, Structural Genomics, Psi-2, Protein Structure Initiative, Integrated Center For Structure And Function Innovation, Isfi, Tb Structural Genomics Consortium, Tbsgc, Toxin-Antitoxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Miallau, M. Faller, J. Chiang, M. Arbing, F. Guo, D. Cascio, D. Eisenberg
Structure And Proposed Activity Of A Member Of The Vapbc Family Of Toxin-Antitoxin Systems: Vapbc-5 From Mycobacterium Tuberculosis.
J. Biol. Chem. V. 284 276 2009
PubMed-ID: 18952600  |  Reference-DOI: 10.1074/JBC.M805061200

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Atcc: 25618
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET46DUET
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RV0626, MT0654
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
 
Molecule 2 - UNCHARACTERIZED PROTEIN
    Atcc: 25618
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET46DUET
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RV0627
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3NA4Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:25 , THR B:50 , THR B:51 , THR B:54 , ILE B:118BINDING SITE FOR RESIDUE NA B 301
2AC2SOFTWARELEU B:127 , SER B:144 , GLU B:146BINDING SITE FOR RESIDUE NA B 302
3AC3SOFTWARELEU B:78BINDING SITE FOR RESIDUE NA B 303
4AC4SOFTWARELEU B:63 , ALA B:65 , ARG B:71BINDING SITE FOR RESIDUE NA B 304
5AC5SOFTWAREGLU B:79 , ALA B:82BINDING SITE FOR RESIDUE ACT B 305
6AC6SOFTWAREASP B:69 , HIS B:103 , ALA B:142 , ALA B:143BINDING SITE FOR RESIDUE BME B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DBO)

(-) 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:34
 aligned with VAPB5_MYCTO | P9WF18 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:34
                                    55        65        75    
          VAPB5_MYCTO    46 RRWLSKTEFLSRLRGAQADPGLRNDLAVLAGDTT  79
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhh......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 3dbo A  53 RRWLSKTEFLSRLRGAQADPGLRNDLAVLAGDTT  86
                                    62        72        82    


Chain A from PDB  Type:PROTEIN  Length:34
 aligned with VAPB5_MYCTU | P9WF19 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:34
                                    55        65        75    
          VAPB5_MYCTU    46 RRWLSKTEFLSRLRGAQADPGLRNDLAVLAGDTT  79
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhh......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 3dbo A  53 RRWLSKTEFLSRLRGAQADPGLRNDLAVLAGDTT  86
                                    62        72        82    


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with VAPC5_MYCTU | P96917 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:131
                                    14        24        34        44        54        64        74        84        94       104       114       124       134 
          VAPC5_MYCTU     5 PAAGVLDTSVFIATESGRQLDEALIPDRVATTVVTLAELRVGVLAAATTDIRAQRLATLESVADMETLPVDDDAARMWARLRIHLAESGRRVRINDLWIAAVAASRALPVITQDDDFAALDGAASVEIIRV 135
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhh.-----..hhhhh..eeeeehhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....ee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...eee...hhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbo B  20 PAAGVLDTSVFIA-----QLDEALIPDRVATTVVTLAELRVGVLAAATTDIRAQRLATLESVADMETLPVDDDAARMWARLRIHLAESGRRVRINDLWIAAVAASRALPVITQDDDFAALDGAASVEIIRV 150
                                    29  |     39        49        59        69        79        89        99       109       119       129       139       149 
                                       32    38
   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 3DBO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VAPB5_MYCTO | P9WF18)

Chain A   (VAPB5_MYCTU | P9WF19)
molecular function
    GO:0015643    toxic substance binding    Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
    GO:0045927    positive regulation of growth    Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.

Chain B   (VAPC5_MYCTU | P96917)
molecular function
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0040008    regulation of growth    Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 3dbo)
 

(-) 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
  3dbo
    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
  VAPB5_MYCTO | P9WF18
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  VAPB5_MYCTU | P9WF19
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  VAPC5_MYCTU | P96917
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  VAPB5_MYCTO | P9WF18
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  VAPB5_MYCTU | P9WF19
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  VAPC5_MYCTU | P96917
    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 3DBO)

(-) Related Entries Specified in the PDB File

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