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
(-)Biological Unit 3
(-)Biological Unit 4
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF KORA-OPERATOR DNA COMPLEX (KORA-OA)
 
Authors :  S. A. White, E. I. Hyde, K. V. Rajasekar
Date :  16 Jul 15  (Deposition) - 06 Apr 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Biol. Unit 3:  I,J,K,L  (1x)
Biol. Unit 4:  M,N,O,P  (1x)
Keywords :  Helix-Turn-Helix, Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. V. Rajasekar, A. L. Lovering, F. Dancea, D. J. Scott, S. A. Harris, L. E. Bingle, M. Roessle, C. M. Thomas, E. I. Hyde, S. A. White
Flexibility Of Kora, A Plasmid-Encoded, Global Transcriptio Regulator, In The Presence And The Absence Of Its Operator.
Nucleic Acids Res. V. 44 4947 2016
PubMed-ID: 27016739  |  Reference-DOI: 10.1093/NAR/GKW191
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: KORA
    Gene: TRFB, KORA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: REGULATORY PROTEIN KORA
 
Molecule 2 - 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP* GP*GP*)-3'
    Chains: C, D, G, H, K, L, O, P
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES
 
Molecule 3 - TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN
    Chains: E, F, I, J, M, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Gene: TRFB, KORA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: REGULATORY PROTEIN KORA

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric Unit : ABCDEFGHIJKLMNOP
Biological Unit 1 (1x): ABCD            
Biological Unit 2 (1x):     EFGH        
Biological Unit 3 (1x):         IJKL    
Biological Unit 4 (1x):             MNOP

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5CLV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn B:66 -Leu B:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CLV)

(-) 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:95
                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  5clv A  2 KKRLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDKNLPEGYARVTAVLPEHQAYIVRKWEADAKKK 96
                                    11        21        31        41        51        61        71        81        91     


Chain B from PDB  Type:PROTEIN  Length:96
                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......eeeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                  5clv B  2 KKRLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDKNLPEGYARVTAVLPEHQAYIVRKWEADAKKKQ 97
                                    11        21        31        41        51        61        71        81        91      


Chain C from PDB  Type:DNA  Length:20
                                                   
                  5clv C  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20


Chain D from PDB  Type:DNA  Length:20
                                                   
                  5clv D  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20


Chain E from PDB  Type:PROTEIN  Length:65
                                                                                                
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  5clv E  2 KKRLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDKN 66
                                    11        21        31        41        51        61     


Chain F from PDB  Type:PROTEIN  Length:64
                                                                                               
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  5clv F  2 KKRLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDK 65
                                    11        21        31        41        51        61    


Chain G from PDB  Type:DNA  Length:20
                                                   
                  5clv G  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20


Chain H from PDB  Type:DNA  Length:20
                                                   
                  5clv H  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20


Chain I from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  5clv I  4 RLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDK 65
                                    13        23        33        43        53        63  


Chain J from PDB  Type:PROTEIN  Length:63
                                                                                              
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  5clv J  3 KRLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDK 65
                                    12        22        32        42        52        62   


Chain K from PDB  Type:DNA  Length:20
                                                   
                  5clv K  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20


Chain L from PDB  Type:DNA  Length:20
                                                   
                  5clv L  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20


Chain M from PDB  Type:PROTEIN  Length:63
                                                                                              
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                  5clv M  2 KKRLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFED 64
                                    11        21        31        41        51        61   


Chain N from PDB  Type:PROTEIN  Length:64
                                                                                               
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  5clv N  2 KKRLTESQFQEAIQGLEVGQQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFEDK 65
                                    11        21        31        41        51        61    


Chain O from PDB  Type:DNA  Length:20
                                                   
                  5clv O  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20


Chain P from PDB  Type:DNA  Length:20
                                                   
                  5clv P  1 CCAAGTTTAGCTAAACTTGG 20
                                    10        20
   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 5CLV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

 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 5clv)
 
  Sites
(no "Sites" information available for 5clv)
 
  Cis Peptide Bonds
    Asn B:66 - Leu B:67   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 3 PNG format | Biol. Unit 4 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
  5clv
    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
  KORA2_ECOLX | P03052
    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
  KORA2_ECOLX | P03052
    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
        KORA2_ECOLX | P03052: 2n5g 2w7n 5ckt 5cm3

(-) Related Entries Specified in the PDB File

5ckt 5CKT CONTAINS THE SAME PROTEIN IN THE ABSENCE OF DNA