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 :  MOBM RELAXASE DOMAIN (MOBV; MOB_PRE) BOUND TO PLASMID PMV158 ORIT DNA (22NT+3'PHOSPHATE). MN-BOUND CRYSTAL STRUCTURE AT PH 4.6
 
Authors :  R. Pluta, D. R. Boer, M. Coll
Date :  26 Jul 13  (Deposition) - 24 Sep 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Mob Relaxase Family, Mobv, Relaxase/Endonuclease, Orit Dna, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pluta, D. R. Boer, S. Russi, C. Fernandez-Lopez, F. Lorenzo-Diaz, R. Perez-Luque, M. Espinosa, M. Coll
Structures Of Dna-Mobm Relaxase Complexes Reveal A Histidine/Metal Catalysis For Dna Cleavage And Ligation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PLASMID RECOMBINATION ENZYME
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RELAXASE DOMAIN OF MOBM PROTEIN
    Gene: PRE, MOB
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 1311
    Synonym: MOBILIZATION PROTEIN
 
Molecule 2 - ACTTTAT OLIGONUCLEOTIDE
    Chains: B
    Engineered: YES
    Fragment: OLIGONUCLEOTIDE_1 MIMICKING PMV158 ORIT DNA HAIRPIN
    Other Details: OLIGONUCLEOTIDES WERE OBTAINED FROM BIOMERS (ULM, GERMANY).
    Synthetic: YES
 
Molecule 3 - ATAAAGTATAGTGTGPO OLIGONUCLEOTIDE
    Chains: C
    Engineered: YES
    Fragment: OLIGONUCLEOTIDE_2 MIMICKING PMV158 ORIT DNA HAIRPIN
    Other Details: OLIGONUCLEOTIDES WERE OBTAINED FROM BIOMERS (ULM, GERMANY).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:126 , GLU A:129 , HIS A:133 , HIS A:135 , DG C:26 , DT C:27BINDING SITE FOR RESIDUE MN A 201
2AC2SOFTWAREDT B:3BINDING SITE FOR RESIDUE NA B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LVK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LVK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LVK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LVK)

(-) Exons   (0, 0)

(no "Exon" information available for 4LVK)

(-) 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:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeehhhhhhhhhhhhh.......hhhhhhhhee........hhhhhhhhhhhhhh............eeeeeee.hhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeee..ee..eehhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lvk A   2 SYMVARMQKMKAGNLGGAFKHNERVSNKDINPSRSHLNYELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKDFFEKLDEEQTRTFFETAKNYFAENYGESNIAYASVHLDESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPRYMSDHGFELERGKLNSEAKHKTVAEFKRAM 196
                                    11        21    ||  35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
                                                   26|                                                                                                                                                                     
                                                    31                                                                                                                                                                     


Chain B from PDB  Type:DNA  Length:7
                                       
                 4lvk B   1 ACTTTAT   7


Chain C from PDB  Type:DNA  Length:16
                                                
                 4lvk C  12 ATAAAGTATAGTGTGT  27
                                    21
   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 4LVK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LVK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LVK)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4lvk)
 

(-) 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
  4lvk
    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
  PRE_STRAG | P13925
    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
  PRE_STRAG | P13925
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRE_STRAG | P13925: 4lvi 4lvj 4lvl 4lvm 5n2q

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4LVK)