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

(-) Description

Title :  STRUCTURE OF REP-DNA COMPLEX
 
Authors :  M. Schumacher
Date :  03 Jun 16  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,R,W
Biol. Unit 1:  A,B,C,H,R,W  (1x)
Biol. Unit 2:  D,E,F,G  (1x)
Keywords :  Replication Initiation, Rep Protein, S. Aureus, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, N. K. Tonthat, S. M. Kwong, N. B. Chinnam, M. A. Liu, R. A. Skurray, N. Firth
Mechanism Of Staphylococcal Multiresistance Plasmid Replication Origin Assembly By The Repa Protein.
Proc. Natl. Acad. Sci. V. 111 9121 2014 U. S. A.
PubMed-ID: 24927575  |  Reference-DOI: 10.1073/PNAS.1406065111

(-) Compounds

Molecule 1 - REPLICATION INITIATOR A, N-TERMINAL
    Chains: A, B, C, H, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-133
    Gene: SAP042A_013, SAP058A_012, SAP071A_014
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
 
Molecule 2 - DNA (32-MER)
    Chains: R
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (32-MER)
    Chains: W
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHRW
Biological Unit 1 (1x): ABC    HRW
Biological Unit 2 (1x):    DEFG   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5KBJ)

(-) Sites  (0, 0)

(no "Site" information available for 5KBJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KBJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KBJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KBJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KBJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5KBJ)

(-) 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:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh..hhhhhhhhhhhhhh...eeee........eeee.....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj A   4 QYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDVEPY 133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133


Chain B from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.............hhhhhhhhh..hhhhhhhhhhhhhhh..eeee........eeee.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj B   4 QYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDVEPY 133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.eeeeehhhhhh......hhhhhhhhhhhhhhhhhhhhh.........eee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eee....eeee.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj C   4 QYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRPNILYLMKPIVTERDIYKIEKEENDVEPY 133
                                    13        23        33        43        53        63        73        83        93     ||108       118       128     
                                                                                                                          99|                            
                                                                                                                          105                            


Chain D from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...eeeeehhhhhh......hhhhhhhhhhhh.hhhhhhhh.............hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee........eeee.....hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj D   4 QYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDVEPY 133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133


Chain E from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..........eeehhhhhhhhh..hhhhhhhhhhhhhhhh.eeee.......eeeee.....hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj E   4 QYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDVEPY 133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133


Chain F from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...eeeee............hhhhhhhhhhhhhhhhhhhhh.........ee..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee........eeee.....hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj F   4 QYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDVEPY 133
                                    13        23        33        43        53        63        73        83        93       103       113       123       133


Chain G from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...eeeee.hhh........hhhhhhhhhhhhhhhhhhhhh...............hhhhhhh....hhhhhhhhhh..........................hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj G   2 QNQYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDV 130
                                    11        21        31        41        51        61        71        81        91       101       111       121         


Chain H from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.eeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...........ee..hhhhhhhhh..hhhhhhhhhh.......eeee........eeee.....hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kbj H   4 QYFTVQENYKERFYQIPKVFFTSENYKNLTNDMKIAYAILRDRLNLSIKNSWVDEDGNIYFVYSNEKLMEILNCKKEKLTKIKKGLENDGLLIQKRRGLNKPNILYLMKPIVTERDIYKIEKEENDV 130
                                    13        23        33        43        53        63        73        83        93       103       113       123       


Chain R from PDB  Type:DNA  Length:32
                                                                
                 5kbj R   2 CGTCCAGAAGTTCGAAAATCGAACGTCCAGAT  33
                                    11        21        31  


Chain W from PDB  Type:DNA  Length:32
                                                                
                 5kbj W   3 ATCTGGACGTTCGATTTTCGAACTTCTGGACG  34
                                    12        22        32
   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 5KBJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KBJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KBJ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5KBJ)

 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
(no "Ligands, Modified Residues, Ions" information available for 5kbj)
 
  Sites
(no "Sites" information available for 5kbj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5kbj)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  5kbj
    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
  D2JDC3_STAAU | D2JDC3
    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
  D2JDC3_STAAU | D2JDC3
    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 5KBJ)

(-) Related Entries Specified in the PDB File

4pqk 4pql 4pt7 4pta