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 :  CRYSTAL STRUCTURE OF THE METHYLENE BLUE-BOUND FORM OF THE MULTI-DRUG BINDING TRANSCRIPTIONAL REPRESSOR CGMR
 
Authors :  H. Itou, Y. Shirakihara, I. Tanaka
Date :  12 Apr 07  (Deposition) - 15 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcriptional Regulator, Helix-Turn-Helix, Tetr-Family, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Itou, N. Watanabe, M. Yao, Y. Shirakihara, I. Tanaka
Crystal Structures Of The Multidrug Binding Repressor Corynebacteriumglutamicum Cgmr In Complex With Inducers And With An Operator
J. Mol. Biol. V. 403 174 2010
PubMed-ID: 20691702  |  Reference-DOI: 10.1016/J.JMB.2010.07.042

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGL2612
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 196627
    Strain: ATCC13032
    Synonym: BACTERIAL REGULATORY PROTEIN, TETR FAMILY, CGL2612

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3MBT2Ligand/Ion3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:5 , LYS A:6 , ASN A:129 , ALA A:131 , HOH A:3092BINDING SITE FOR RESIDUE CL A 3001
2AC2SOFTWARETRP A:63 , GLU A:66 , THR A:87 , LEU A:88 , GLU A:96 , TRP A:113 , PHE A:147 , HOH A:3010BINDING SITE FOR RESIDUE MBT A 1001
3AC3SOFTWAREILE A:152 , TRP B:63 , GLU B:66 , THR B:87 , LEU B:88 , GLU B:90 , GLU B:96 , TRP B:113 , PHE B:147 , HOH B:2017BINDING SITE FOR RESIDUE MBT B 1002
4AC4SOFTWAREALA A:131 , ARG A:134 , HOH A:3060 , THR B:168BINDING SITE FOR RESIDUE GOL A 2003
5AC5SOFTWAREALA A:50 , LEU A:53 , GLU A:57 , HOH A:3102 , HOH A:3118BINDING SITE FOR RESIDUE GOL A 2004
6AC6SOFTWAREARG A:82 , LEU A:170 , HOH A:3041 , HOH A:3051 , HOH A:3126 , HIS B:49 , HIS B:106 , HOH B:2092BINDING SITE FOR RESIDUE GOL A 2005
7AC7SOFTWARELEU A:100 , ALA A:103 , PRO A:104 , ASN A:117 , TYR B:151 , ILE B:152 , HIS B:153 , HOH B:2095BINDING SITE FOR RESIDUE GOL B 2001
8AC8SOFTWARETHR B:12 , ASP B:15 , ALA B:33 , HOH B:2105BINDING SITE FOR RESIDUE GOL B 2002
9AC9SOFTWAREASP A:69 , HOH A:3020 , HOH A:3066 , ASN B:117 , HIS B:118 , ILE B:121 , THR B:124 , HOH B:2016 , HOH B:2070 , HOH B:2076 , HOH B:2132BINDING SITE FOR RESIDUE GOL B 2006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YVE)

(-) 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:175
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
         Q8NMG3_CORGL     1 MRTSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIPS 175
               SCOP domains d2yvea1 A:1-74 Transcriptional regulator Cgl2612                          d2yvea2 A:75-175 Transcriptional regulator Cgl2612                                                    SCOP domains
               CATH domains 2yveA00 A:1-175 Tetracycline Repressor, domain 2                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yve A   1 MRTSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIPS 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with Q8NMG3_CORGL | Q8NMG3 from UniProtKB/TrEMBL  Length:177

    Alignment length:172
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  
         Q8NMG3_CORGL     3 TSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
               SCOP domains d2yveb1 B:3-74 Transcriptional regulator Cgl2612                        d2yveb2 B:75-174 Transcriptional regulator Cgl2612                                                   SCOP domains
               CATH domains 2yveB00 B:3-174 Tetracycline Repressor, domain 2                                                                                                                             CATH domains
           Pfam domains (1) ------TetR_N-2yveB01 B:9-55                          ----------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------TetR_N-2yveB02 B:9-55                          ----------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yve B   3 TSKKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRHALLLGMHELLADDWDKELRDITRDPEDPLERLRAVVVTLAENVSRPELLLLIDAPSHPDFLNAWRTVNHQWIPDTDDLENDAHKRAVYLVQLAADGLFVHDYIHDDVLSKSKRQAMLETILELIP 174
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   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, 4)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8NMG3_CORGL | Q8NMG3)
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/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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MBT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yve)
 

(-) 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
  2yve
    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
  Q8NMG3_CORGL | Q8NMG3
    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
  Q8NMG3_CORGL | Q8NMG3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8NMG3_CORGL | Q8NMG3: 2yvh 2zoy 2zoz

(-) Related Entries Specified in the PDB File

2yvh THE SAME PROTEIN BOUND TO DNA
2zoy THE SAME PROTEIN IN LIGAND-FREE STATE
2zoz THE SAME PROTEIN COMPLEXED WITH ETHIDIUM