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(-) Description

Title :  STAPHYLOCOCCUS EPIDERMIDIS TCAR IN COMPLEX WITH KANAMYCIN
 
Authors :  Y. M. Chang, C. K. Chen, A. H. Wang
Date :  15 Nov 09  (Deposition) - 09 Jun 10  (Release) - 09 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Multiple Drug Resistance, Biofilm, Transcription Regulation, Dna Binding, Antibiotics, Transcription, Transcription Regulator- Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. M. Chang, W. Y. Jeng, T. P. Ko, Y. J. Yeh, C. K. Chen, A. H. Wang
Structural Study Of Tcar And Its Complexes With Multiple Antibiotics From Staphylococcus Epidermidis.
Proc. Natl. Acad. Sci. Usa V. 107 8617 2010
PubMed-ID: 20421503  |  Reference-DOI: 10.1073/PNAS.0913302107

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR TCAR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SERP1949, SE_1937, TCAR
    Organism Scientific: STAPHYLOCOCCUS EPIDERMIDIS RP62A
    Organism Taxid: 176279
    Strain: ATCC 35984

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1KAN2Ligand/IonKANAMYCIN A

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:19 , ASN A:20 , THR A:23 , GLN A:31 , ALA A:38 , GLU A:39 , SER A:41 , HIS A:42 , GLN A:61 , ARG A:110 , GLU B:13 , ASN B:17 , GLN B:61BINDING SITE FOR RESIDUE KAN A 2001
2AC2SOFTWAREASP A:29 , GLU B:33 , TYR B:34 , ALA B:66 , ARG B:70 , LYS B:74 , LYS B:102 , LYS B:105BINDING SITE FOR RESIDUE KAN B 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KP5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KP5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KP5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KP5)

(-) Exons   (0, 0)

(no "Exon" information available for 3KP5)

(-) 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:136
 aligned with Q5HLN6_STAEQ | Q5HLN6 from UniProtKB/TrEMBL  Length:151

    Alignment length:148
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143        
         Q5HLN6_STAEQ     4 RIEDHISFLEKFINDVNTLTAKLLKDLQTEYGISAEQSHVLNMLSIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKERKAIMSHIASDMTSDFDSKEIEKVRQVLEIIDYRIQSYTSKL 151
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhh......------------....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kp5 A   4 RIEDHISFLEKFINDVNTLTAKLLKDLQTEYGISAEQSHVLNMLSIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKL------------IIKLSNKGKKYIKERKAIMSHIASDMTSDFDSKEIEKVRQVLEIIDYRIQSYTSKL 151
                                    13        23        33        43        53        63        73        83         -  |    103       113       123       133       143        
                                                                                                          83           96                                                       


Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q5HLN6_STAEQ | Q5HLN6 from UniProtKB/TrEMBL  Length:151

    Alignment length:147
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       
         Q5HLN6_STAEQ     5 IEDHISFLEKFINDVNTLTAKLLKDLQTEYGISAEQSHVLNMLSIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKERKAIMSHIASDMTSDFDSKEIEKVRQVLEIIDYRIQSYTSKL 151
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------MarR_2-3kp5B01 B:34-84                             ------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------MarR_2-3kp5B02 B:34-84                             ------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh..eee.----------..eeehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kp5 B   5 IEDHISFLEKFINDVNTLTAKLLKDLQTEYGISAEQSHVLNMLSIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKLE----------KIIKLSNKGKKYIKERKAIMSHIASDMTSDFDSKEIEKVRQVLEIIDYRIQSYTSKL 151
                                    14        24        34        44        54        64        74        84         -|      104       114       124       134       144       
                                                                                                          84         95
   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 3KP5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KP5)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5HLN6_STAEQ | Q5HLN6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5HLN6_STAEQ | Q5HLN6: 3kp2 3kp3 3kp4 3kp6 3kp7 4ejt 4eju 4ejv 4ejw

(-) Related Entries Specified in the PDB File

3kp2 3kp3 3kp4 3kp6 3kp7