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 SOX-DNA COMPLEX
 
Authors :  C. Bagneris, T. E. Barrett
Date :  23 Nov 10  (Deposition) - 21 Sep 11  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Type Ii Restriction Endonuclease Superfamily, Nuclease, Nucleus/Cytoplasm, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bagneris, L. C. Briggs, R. Savva, B. Ebrahimi, T. E. Barrett
Crystal Structure Of A Kshv-Sox-Dna Complex: Insights Into The Molecular Mechanisms Underlying Dnase Activity And Host Shutoff
Nucleic Acids Res. V. 39 5744 2011
PubMed-ID: 21421561  |  Reference-DOI: 10.1093/NAR/GKR111

(-) Compounds

Molecule 1 - ORF 37
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM6T1
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ORF37
    Organism Scientific: HUMAN HERPESVIRUS 8 TYPE M
    Organism Taxid: 435895
 
Molecule 2 - DNA (5'- D(*GP*GP*GP*AP*TP*CP*CP*TP*CP*CP*CP*AP*GP*TP*CP*GP*AP*CP*C)-3')
    Chains: C
    Engineered: YES
    Other Details: DNA SYNTHESISED BY EUROGENTEC
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*GP*GP*TP*CP*GP*AP*CP*TP*AP*GP*GP*AP*GP*GP*AP*TP*CP*CP*C)-3')
    Chains: D
    Engineered: YES
    Other Details: DNA SYNTHESISED BY EUROGENTEC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:184 , ASP A:221 , GLU A:244 , ILE A:245 , LYS A:246BINDING SITE FOR RESIDUE MG A 487
2AC2SOFTWAREGLU A:184 , LYS A:246 , CYS A:247 , HOH A:523 , DG C:3BINDING SITE FOR RESIDUE MG A 488
3AC3SOFTWARESER A:145 , VAL A:218 , SER A:219BINDING SITE FOR RESIDUE FMT A 489

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:59 -Pro A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3POV)

(-) 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:445
 aligned with P88925_HHV8 | P88925 from UniProtKB/TrEMBL  Length:486

    Alignment length:478
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473        
          P88925_HHV8     4 TPTPADLFSEDYLVDTLDGLTVDDQQAVLASLSFSKFLKHAKVRDWCAQAKIQPSMPALRMAYNYFLFSKVGEFIGSEDVCNFFVDRVFGGVRLLDVASVYAACSQMNAHQRHHICCLVERATSSQSLNPVWDALRDGIISSSKFHWAVKQQNTSKKIFSPWPITNNHFVAGPLAFGLRCEEVVKTLLATLLHPDETNCLDYGFMQSPQNGIFGVSLDFAANVKTDTEGRLQFDPNCKVYEIKCRFKYTFAKMECDPIYAAYQRLYEAPGKLALKDFFYSISKPAVEYVGLGKLPSESDYLVAYDQEWEACPRKKRKLTPLHNLIRECILHNSTTESDVYVLTDPQDTRGQISIKARFKANLFVNVRHSYFYQVLLQSSIVEEYIGLDSGIPRLGSPKYYIATGFFRKRGYQDPVNCTIGGDALDPHVEIPTLLIVTPVYFPRGAKHRLLHQAANFWSRSAKDTFPYIKWDFSYLSAN 481
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh..----.....-------------hhhhhhhhhhhhhhhhh......ee.....ee......eee...eee....-------.....eeeeeeee..........hhhhhhhhhhhhh.hhhhhhhhhh......eee............eee.hhhhh.........hhhhhhhhhhhhh.....eeeeee...........eeeeeee..ee...hhhhhhhhhhhhhhhhh..---------..eeeeeeeeee..........ee..ee......eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh........hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pov A   4 TPTPADLFSEDYLVDTLDGLTVDDQQAVLASLSFSKFLKHAKVRDWCAQAKIQPSMPALRMAYNYFLFSKVGEFIGSEDVCNFFVDRVFGGVRLLDVASVYAACSQMNAHQRHHICCLVERATSSQSLNPVWDALRDGIISSSKFHWAVKQQ----KIFSP-------------AFGLRCEEVVKTLLATLLHPDETNCLDYGFMQSPQNGIFGVSLDFAANVKT-------FDPNCKVYEIKCRFKYTFAKMECDPIYAAYQRLYEAPGKLALKDFFYSISKPAVEYVGLGKLPSESDYLVAYDQEWEACPRKKRKLTPLHNLIRECILHNSTTESDVYVLTDPQDTRGQISIKARFKANLFVNVRHSYFYQVLLQSSIVEEYIG---------SPKYYIATGFFRKRGYQDPVNCTIGGDALDPHVEIPTLLIVTPVYFPRGAKHRLLHQAANFWSRSAKDTFPYIKWDFSYLSAN 481
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153 |    |163|        -    |  183       193       203       213       223    |    -  |    243       253       263       273       283       293       303       313       323       333       343       353       363       373       383     |   -     | 403       413       423       433       443       453       463       473        
                                                                                                                                                                                 155  160 164           178                                               228     236                                                                                                                                                      389       399                                                                                  


Chain C from PDB  Type:DNA  Length:19
                                                   
                 3pov C   2 GGGATCCTCCCAGTCGACC  20
                                    11         


Chain D from PDB  Type:DNA  Length:19
                                                   
                 3pov D  21 GGTCGACTAGGAGGATCCC  39
                                    30
   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 3POV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P88925_HHV8 | P88925)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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: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).
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

 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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:59 - Pro A:60   [ RasMol ]  
 

(-) 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
  3pov
    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
  P88925_HHV8 | P88925
    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
  P88925_HHV8 | P88925
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        P88925_HHV8 | P88925: 3fhd 5hsw

(-) Related Entries Specified in the PDB File

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