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 :  HIGH RESOLUTION STRUCTURE OF NATIVE CYLR2
 
Authors :  T. Gruene, M. -K. Cho, I. Karyagina, H. -Y. Kim, C. Grosse, K. Giller, M. Zweckstetter, S. Becker
Date :  28 Jun 10  (Deposition) - 09 Feb 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.21
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Hth Dna-Binding Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Gruene, M. K. Cho, I. Karyagina, H. Y. Kim, C. Grosse, K. Giller, M. Zweckstetter, S. Becker
Integrated Analysis Of The Conformation Of A Protein-Linked Spin Label By Crystallography, Epr And Nmr Spectroscopy.
J. Biomol. Nmr V. 49 111 2011
PubMed-ID: 21271275  |  Reference-DOI: 10.1007/S10858-011-9471-Y

(-) Compounds

Molecule 1 - PUTATIVE TRANSCRIPTION REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Synonym: CYTOLYSIN REPRESSOR 2, CYLR2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:42 , LEU A:43 , GLN A:44 , TYR A:51 , HOH A:2068 , HOH A:2087 , ASN B:40BINDING SITE FOR RESIDUE GOL A1067
2AC2SOFTWARESER A:18 , ARG A:28 , HOH A:2032 , HOH A:2044 , HOH A:2088 , HOH B:2030BINDING SITE FOR RESIDUE GOL A1068
3AC3SOFTWARELEU B:8 , GLU B:11 , LYS B:12 , HOH B:2069BINDING SITE FOR RESIDUE GOL B1067

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XI8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XI8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XI8)

(-) Exons   (0, 0)

(no "Exon" information available for 2XI8)

(-) 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:66
 aligned with Q8VL32_ENTFL | Q8VL32 from UniProtKB/TrEMBL  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
          Q8VL32_ENTFL    1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE 66
               SCOP domains d2xi8a_ A: Putative transcription regulator CylR2                  SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhheee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2xi8 A  1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE 66
                                    10        20        30        40        50        60      


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with Q8VL32_ENTFL | Q8VL32 from UniProtKB/TrEMBL  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
          Q8VL32_ENTFL    1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE 66
               SCOP domains d2xi8b_ B: Putative transcription regulator CylR2                  SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eehhhhhhhhh..hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  2xi8 B  1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE 66
                                    10        20        30        40        50        60
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XI8)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8VL32_ENTFL | Q8VL32)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xi8)
 

(-) 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
  2xi8
    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
  Q8VL32_ENTFL | Q8VL32
    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
  Q8VL32_ENTFL | Q8VL32
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8VL32_ENTFL | Q8VL32: 1utx 2gzu 2lyj 2lyk 2lyl 2lyp 2lyq 2lyr 2lys 2xiu 2xj3

(-) Related Entries Specified in the PDB File

1utx REGULATION OF CYTOLYSIN EXPRESSION BY ENTEROCOCCUS FAECALIS: ROLE OF CYLR2
2xiu HIGH RESOLUTION STRUCTURE OF MTSL-TAGGED CYLR2.
2xj3 HIGH RESOLUTION STRUCTURE OF THE T55C MUTANT OF CYLR2.