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 :  THE CRYSTAL STRUCTURE OF THE PAS DOMAIN IN COMPLEX WITH ETHANOL OF A TRANSCRIPTIONAL REGULATOR IN THE LUXR FAMILY FROM BURKHOLDERIA THAILANDENSIS TO 1.65A
 
Authors :  A. J. Stein, C. Tesar, K. Buck, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  28 Apr 10  (Deposition) - 23 Jun 10  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pas Domain, Luxr, Regulator, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, C. Tesar, K. Buck, A. Joachimiak
The Crystal Structure Of The Pas Domain In Complex With Ethanol Of A Transcriptional Regulator In The Luxr Family From Burkholderia Thailandensis To 1. 65A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, LUXR FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: SEQUENCE DATABASE RESIDUES 2-121
    Gene: BTH_I2609
    Organism Scientific: BURKHOLDERIA THAILANDENSIS
    Organism Taxid: 271848
    Strain: E264

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2EOH4Ligand/IonETHANOL
3MSE4Mod. Amino AcidSELENOMETHIONINE
4NA2Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:23 , PHE A:48 , TYR A:52 , HOH A:135BINDING SITE FOR RESIDUE EOH A 1
2AC2SOFTWAREHIS A:72 , SER A:74 , TYR A:75 , ALA A:76 , ARG B:119BINDING SITE FOR RESIDUE EOH A 122
3AC3SOFTWARESER A:54 , SER A:55BINDING SITE FOR RESIDUE EDO A 123
4AC4SOFTWAREGLU A:26 , ASP A:27 , ILE B:4 , TYR B:6BINDING SITE FOR RESIDUE EDO A 124
5AC5SOFTWARESER A:20 , ASP A:22 , ARG A:23 , LEU A:104 , ALA A:105 , HOH A:135BINDING SITE FOR RESIDUE NA A 125
6AC6SOFTWAREARG B:23 , PHE B:48 , TYR B:52 , HOH B:146BINDING SITE FOR RESIDUE EOH B 122
7AC7SOFTWAREGLU B:31 , ALA B:34 , ILE B:35 , ARG B:37 , ASP B:113BINDING SITE FOR RESIDUE EOH B 123
8AC8SOFTWARESER B:55BINDING SITE FOR RESIDUE EDO B 124
9AC9SOFTWARESER B:20 , ASP B:22 , ARG B:23 , LEU B:104 , ALA B:105 , HOH B:146BINDING SITE FOR RESIDUE NA B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MQQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MQQ)

(-) 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:113
 aligned with Q2SVC5_BURTA | Q2SVC5 from UniProtKB/TrEMBL  Length:181

    Alignment length:113
                                    13        23        33        43        53        63        73        83        93       103       113   
         Q2SVC5_BURTA     4 IDYKTAFHLAPIGLVLSRDRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRALDRTAPLAAGVWTFEDLSA 116
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..eeeeee..eeeeehhhhhhhh..hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeeee.....eeeeeeeeee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3mqq A   4 IDYKTAFHLAPIGLVLSRDRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVmIAHGSYADDRImKRAGGELFWCHVTGRALDRTAPLAAGVWTFEDLSA 116
                                    13        23        33        43        53        63     |  73       |83        93       103       113   
                                                                                            69-MSE      81-MSE                               


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with Q2SVC5_BURTA | Q2SVC5 from UniProtKB/TrEMBL  Length:181

    Alignment length:118
                                    13        23        33        43        53        63        73        83        93       103       113        
         Q2SVC5_BURTA     4 IDYKTAFHLAPIGLVLSRDRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVMIAHGSYADDRIMKRAGGELFWCHVTGRALDRTAPLAAGVWTFEDLSATRRVA 121
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------PAS_9-3mqqB01 B:15-116                                                                                ----- Pfam domains (1)
           Pfam domains (2) -----------PAS_9-3mqqB02 B:15-116                                                                                ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhh..eeeeee..eeeeehhhhhhhh..hhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeeeee.....eeeeeeeeee.........eeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3mqq B   4 IDYKTAFHLAPIGLVLSRDRVIEDCNDELAAIFRCARADLIGRSFEVLYPSSDEFERIGERISPVmIAHGSYADDRImKRAGGELFWCHVTGRALDRTAPLAAGVWTFEDLSATRRVA 121
                                    13        23        33        43        53        63     |  73       |83        93       103       113        
                                                                                            69-MSE      81-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  (0, 0)

(no "SCOP Domain" information available for 3MQQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MQQ)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2SVC5_BURTA | Q2SVC5)
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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EOH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 3mqq)
 

(-) 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
  3mqq
    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
  Q2SVC5_BURTA | Q2SVC5
    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
  Q2SVC5_BURTA | Q2SVC5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q2SVC5_BURTA | Q2SVC5: 3mqo

(-) Related Entries Specified in the PDB File

3mqo STRUCTURE IN COMPLEX WITH ETHANOL RELATED ID: APC67393.1 RELATED DB: TARGETDB