Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE TRANSCRIPTIONAL REGULATOR (GNTR FAMILY) FROM ENTEROCOCCUS FAECALIS V583
 
Authors :  R. Zhang, M. Zhou, M. Bargassa, Z. Otwinowski, A. Joachimiak, Midwest For Structural Genomics (Mcsg)
Date :  06 Jun 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Transcriptional Regulator (Gntr Family, Structure Genomics, Psi2, Mcsg, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, M. Zhou, M. Bargassa, Z. Otwinowski, A. Joachimiak
The Crystal Structure Of The Transcriptional Regulator (Gnt Family) From Enterococcus Faecalis V583
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR (GNTR FAMILY)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Strain: V583

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:21 , TYR A:129 , ARG A:131BINDING SITE FOR RESIDUE MG A 146
2AC2SOFTWARESER B:21 , TYR B:129 , ARG B:131BINDING SITE FOR RESIDUE MG B 146
3AC3SOFTWARETYR D:129BINDING SITE FOR RESIDUE MG D 146

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:85 -His A:86
2Gly A:136 -Ser A:137
3Gly C:136 -Ser C:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DDV)

(-) 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:121
 aligned with Q835P8_ENTFA | Q835P8 from UniProtKB/TrEMBL  Length:235

    Alignment length:143
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232   
         Q835P8_ENTFA    93 NRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKSGHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLEK 235
               SCOP domains d3ddva1 A:3-145 Transcriptional regulator EF1328                                                                                                SCOP domains
               CATH domains 3ddvA01 A:3-143 Chorismate lyase                                                                                                             -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee..hhhhhhhhh......eeeeeeeeee..eeeeeeeeeee.hhh----------------------....eeeeeeeee.hhhhhhhh......eeeeeeeeee.....eeeeeeeee......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddv A   3 NRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLV----------------------KIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLEK 145
                                    12        22        32        42        52       | -         -         -|       92       102       112       122       132       142   
                                                                                    60                     83                                                              


Chain B from PDB  Type:PROTEIN  Length:139
 aligned with Q835P8_ENTFA | Q835P8 from UniProtKB/TrEMBL  Length:235

    Alignment length:139
                                   106       116       126       136       146       156       166       176       186       196       206       216       226         
         Q835P8_ENTFA    97 SSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKSGHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLEK 235
               SCOP domains d3ddvb_ B: Transcriptional regulator EF1328                                                                                                 SCOP domains
               CATH domains 3ddvB01 B:7-143 Chorismate lyase                                                                                                         -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhh......eeeeeeeeee..eeeeeeeeeee.hhh...hhhhhhhhhhhhhhhhhh..eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee....eeeeeeeeee.hhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ddv B   7 SSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKSGHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLEK 145
                                    16        26        36        46        56        66        76        86        96       106       116       126       136         


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q835P8_ENTFA | Q835P8 from UniProtKB/TrEMBL  Length:235

    Alignment length:144
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231    
         Q835P8_ENTFA    92 QNRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKSGHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLEK 235
               SCOP domains d3ddvc_ C: Transcriptional regulator EF1328                                                                                                      SCOP domains
               CATH domains 3ddvC01 C:2-143 Chorismate lyase                                                                                                              -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeee..hhhhhhhhh......eeeeeeeeee..eeeeeeeeeee.hhh------------------------..eeeeeeeee.hhhhhhhhh.....eeeeeeeeee.....eeeeeeeee.....eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ddv C   2 QNRVPSSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLV------------------------GHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLEK 145
                                    11        21        31        41        51        |-         -         -   |    91       101       111       121       131       141    
                                                                                     60                       85                                                            


Chain D from PDB  Type:PROTEIN  Length:138
 aligned with Q835P8_ENTFA | Q835P8 from UniProtKB/TrEMBL  Length:235

    Alignment length:138
                                   106       116       126       136       146       156       166       176       186       196       206       216       226        
         Q835P8_ENTFA    97 SSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKSGHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLE 234
               SCOP domains d3ddvd_ D: Transcriptional regulator EF1328                                                                                                SCOP domains
               CATH domains 3ddvD01 D:7-143 Chorismate lyase                                                                                                         - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhh......eeeeeeeeee..eeeeeeeeeee.hhh...hhhhhhhhhhhhhhhhhh..eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee....eeeeeeeeee.hhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ddv D   7 SSRTVSYFVAKPSSSEMEKLQLGPEDSILRMERIRFADDIPICFEVASIPYSLVSQYGKSEITNSFYKTLEAKSGHKIGHSNQTISAVQASEQIAEYLEIKRGDAILRVRQVSYFENGLPFEYVRTQYAGSRFEFYLE 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DDV)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q835P8_ENTFA | Q835P8)
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.

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:136 - Ser A:137   [ RasMol ]  
    Gly A:85 - His A:86   [ RasMol ]  
    Gly C:136 - Ser C:137   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  3ddv
    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
  Q835P8_ENTFA | Q835P8
    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
  Q835P8_ENTFA | Q835P8
    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 3DDV)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DDV)