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

(-) Description

Title :  CRYSTAL STRUCTURE OF A TETR FAMILY TRANSCRIPTIONAL REGULATOR (NCGL1578, CGL1640) FROM CORYNEBACTERIUM GLUTAMICUM AT 2.10 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 Dec 06  (Deposition) - 26 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcription Regulator, Dna/Rna-Binding 3-Helical Bundle Fold, Helix Turn Helix Motif, Hth Motif, Transcription Regulation, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Transcriptional Regulator (Np_600854. 1 From Corynebacterium Glutamicum Atcc 13032 Kitasato At 2. 10 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_600854.1
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Synonym: BACTERIAL REGULATORY PROTEINS, TETR FAMILY

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:21 , VAL A:66 , SER A:75 , ARG A:95BINDING SITE FOR RESIDUE UNL A 199
2AC2SOFTWAREGLU A:124BINDING SITE FOR RESIDUE UNL A 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O7T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O7T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O7T)

(-) Exons   (0, 0)

(no "Exon" information available for 2O7T)

(-) 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:188
 aligned with Q8NQ14_CORGL | Q8NQ14 from UniProtKB/TrEMBL  Length:198

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8NQ14_CORGL     1 MRADALKRREHIITTTCNLYRTHHHDSLTMENIAEQAGVGVATLYRNFPDRFTLDMACAQYLFNVVISLQLQAISTFPTDPEGVWTSFNQLLFDRGLGSLVPALAPESLDDLPDEVSALRRTTEKNTTTLINLAKQHGLVHHDIAPGTYIVGLITISRPPITALATISENSHKALLGLYLSGLKHGMM 188
               SCOP domains d2o7ta1 A:1-78 Transcriptional regulator Cgl1640/Cg1846                       d2o7ta2 A:79-188 Transcriptional regulator Cgl1640/Cg1846                                                      SCOP domains
               CATH domains -2o7tA00 A:2-186 Tetracycline Repressor, domain 2                                                                                                                                         -- CATH domains
               Pfam domains -----------TetR_N-2o7tA01 A:12-54                     -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o7t A   1 mRADALKRREHIITTTCNLYRTHHHDSLTmENIAEQAGVGVATLYRNFPDRFTLDmACAQYLFNVVISLQLQAISTFPTDPEGVWTSFNQLLFDRGLGSLVPALAPESLDDLPDEVSALRRTTEKNTTTLINLAKQHGLVHHDIAPGTYIVGLITISRPPITALATISENSHKALLGLYLSGLKHGmm 188
                            |       10        20        30        40        50     |  60        70        80        90       100       110       120       130       140       150       160       170       180      ||
                            |                           30-MSE                    56-MSE                                                                                                                            187-MSE
                            1-MSE                                                                                                                                                                                    188-MSE
   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  (2, 2)

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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8NQ14_CORGL | Q8NQ14)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2o7t)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2o7t
    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
  Q8NQ14_CORGL | Q8NQ14
    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
  Q8NQ14_CORGL | Q8NQ14
    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 2O7T)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2O7T)