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 :  CRYSTAL STRUCTURE OF A TRANSCRIPTIONAL REGULATOR FROM OENOCOCCUS OENI
 
Authors :  R. Zhang, L. Volkart, M. Gu, A. Joachimiak, Midwest Center For Struc Genomics (Mcsg)
Date :  15 Jan 08  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B (1x),E (1x)
Biol. Unit 3:  C  (2x)
Keywords :  Transcriptional Regulator, Structural Genomics, Psi-2, Mcsg, Protein Structure Initiative, Midwest Center For Structural Genomics, Dna- Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, L. Volkart, M. Gu, A. Joachimiak
The Crystal Structure Of A Transcriptional Regulator From Oenococcus Oeni.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PREDICTED TRANSCRIPTIONAL REGULATOR
    Atcc: BAA-331
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: OENOCOCCUS OENI
    Organism Taxid: 203123
    Strain: PSU-1

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A  D 
Biological Unit 2 (1x):  B (1x)  E (1x)
Biological Unit 3 (2x):   C  

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:34 , ARG A:36 , LYS B:43BINDING SITE FOR RESIDUE CA A 203
2AC2SOFTWARETYR B:10BINDING SITE FOR RESIDUE CA B 201
3AC3SOFTWARESER C:34BINDING SITE FOR RESIDUE CA C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BY6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser E:101 -Gly E:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BY6)

(-) Exons   (0, 0)

(no "Exon" information available for 3BY6)

(-) 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:119
 aligned with Q04D30_OENOB | Q04D30 from UniProtKB/TrEMBL  Length:123

    Alignment length:119
                              1                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108         
         Q04D30_OENOB     - --MAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILG 117
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3by6A01 A:-1-74 'winged helix' repressor DNA binding domain                 3by6A02 A:75-117                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.......ee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3by6 A  -1 QAMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILG 117
                                     8        18        28        38        48        58        68        78        88        98       108         


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with Q04D30_OENOB | Q04D30 from UniProtKB/TrEMBL  Length:123

    Alignment length:118
                             1                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109        
         Q04D30_OENOB     - -MAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILG 117
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3by6B01 B:0-74 'winged helix' repressor DNA binding domain                 3by6B02 B:75-117                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh.......ee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3by6 B   0 AMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILG 117
                                     9        19        29        39        49        59        69        79        89        99       109        


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q04D30_OENOB | Q04D30 from UniProtKB/TrEMBL  Length:123

    Alignment length:120
                               1                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117
         Q04D30_OENOB     - ---MAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILG 117
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3by6C01 C:-2-74 'winged helix' repressor DNA binding domain                  3by6C02 C:75-117                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3by6 C  -2 FQAMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILG 117
                                     7        17        27        37        47        57        67        77        87        97       107       117


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with Q04D30_OENOB | Q04D30 from UniProtKB/TrEMBL  Length:123

    Alignment length:121
                              1                                                                                                                      
                              |      8        18        28        38        48        58        68        78        88        98       108       118 
         Q04D30_OENOB     - --MAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILGGK 119
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3by6D01 D:-1-74 'winged helix' repressor DNA binding domain                 3by6D02 D:75-119                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.......ee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3by6 D  -1 QAMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILGGK 119
                                     8        18        28        38        48        58        68        78        88        98       108       118 


Chain E from PDB  Type:PROTEIN  Length:124
 aligned with Q04D30_OENOB | Q04D30 from UniProtKB/TrEMBL  Length:123

    Alignment length:124
                              1                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118    
         Q04D30_OENOB     - --MAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILGGKNAE 122
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3by6E01 E:-1-74 'winged helix' repressor DNA binding domain                 3by6E02 E:75-122                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh.......ee.hhhhhhhhh..hhhhhhhhhhhhhhh..eeee...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3by6 E  -1 QAMAITQKRPVYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKGTFITGNTASVKNSNQNRLLADLSQVIAELIKSGVKGERIKKIVNDILGGKNAE 122
                                     8        18        28        38        48        58        68        78        88        98       108       118
   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 3BY6)

(-) CATH Domains  (2, 10)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BY6)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q04D30_OENOB | Q04D30)
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:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser E:101 - Gly E:102   [ 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
  3by6
    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
  Q04D30_OENOB | Q04D30
    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
  Q04D30_OENOB | Q04D30
    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 3BY6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BY6)