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

(-) Description

Title :  STRUCTURE OF THE REDUCED (FEII) CO-SENSING PROTEIN FROM R. RUBRUM
 
Authors :  W. N. Lanzilotta, D. J. Schuller, T. L. Poulos, M. V. Thorsteinsson, B. Kirby, G. P. Roberts
Date :  12 Sep 00  (Deposition) - 09 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Carbon Monoxide, Heme Sensor, Catabolite Gene Activator Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. N. Lanzilotta, D. J. Schuller, M. V. Thorsteinsson, R. L. Kerby, G. P. Roberts, T. L. Poulos
Structure Of The Co Sensing Transcription Activator Cooa.
Nat. Struct. Biol. V. 7 876 2000
PubMed-ID: 11017196  |  Reference-DOI: 10.1038/82820
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBON MONOXIDE OXIDATION SYSTEM TRANSCRIPTION REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: RHODOSPIRILLUM RUBRUM
    Organism Taxid: 1085
    Synonym: COOA GENE PRODUCT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:74 , CYS A:75 , HIS A:77 , SER A:78 , ILE A:95 , PHE A:98 , GLU A:99 , LEU A:112 , HOH A:357 , PRO B:2 , PRO B:3 , ARG B:4 , TRP B:110 , THR B:121BINDING SITE FOR RESIDUE HEM A 300
2AC2SOFTWAREPRO A:2 , PRO A:3 , ARG A:4 , THR A:121 , MET A:124 , HOH A:325 , HOH A:355 , PHE B:74 , CYS B:75 , HIS B:77 , SER B:78 , ILE B:95 , PHE B:98 , LEU B:112 , LEU B:116BINDING SITE FOR RESIDUE HEM B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FT9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FT9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FT9)

(-) Exons   (0, 0)

(no "Exon" information available for 1FT9)

(-) 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:210
 aligned with P72322_RHORU | P72322 from UniProtKB/TrEMBL  Length:222

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
         P72322_RHORU     2 PPRFNIANVLLSPDGETFFRGFRSKIHAKGSLVCTGEGDENGVFVVVDGRLRVYLVGEEREISLFYLTSGDMFCMHSGCLVEATERTEVRFADIRTFEQKLQTCPSMAWGLIAILGRALTSCMRTIEDLMFHDIKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQGRGHYTIPNLVRLKAAA 213
               SCOP domains d1ft9a2 A:2-133 CO-sensing protein CooA, N-terminal domain                                                                          d1ft9a1 A:134-213 CO-  sensing protein CooA, C-terminal domain                   SCOP domains
               CATH domains 1ft9A01 A:2-132 Jelly Rolls                                                                                                        1ft9A02 A:133-213 'win  ged helix' repressor DNA binding domain                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh...........eeeee....eee........eeeeee.eeeeeeee..eeeeeeeee...eee.....eeee...eeeeeehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........--....ee..hhhhhhhhhh.hhhhhhhhhhhhhhh...ee.....ee..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ft9 A   2 PPRFNIANVLLSPDGETFFRGFRSKIHAKGSLVCTGEGDENGVFVVVDGRLRVYLVGEEREISLFYLTSGDMFCMHSGCLVEATERTEVRFADIRTFEQKLQTCPSMAWGLIAILGRALTSCMRTIEDLMFHDIKQRIAGFFIDHANTTGRQT--GVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQGRGHYTIPNLVRLKAAA 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  |  | 161       171       181       191       201       211  
                                                                                                                                                                                  154  |                                                        
                                                                                                                                                                                     157                                                        


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with P72322_RHORU | P72322 from UniProtKB/TrEMBL  Length:222

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
         P72322_RHORU     2 PPRFNIANVLLSPDGETFFRGFRSKIHAKGSLVCTGEGDENGVFVVVDGRLRVYLVGEEREISLFYLTSGDMFCMHSGCLVEATERTEVRFADIRTFEQKLQTCPSMAWGLIAILGRALTSCMRTIEDLMFHDIKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQGRGHYTIPNLVRLKAAA 213
               SCOP domains d1ft9b2 B:2-133 CO-sensing protein CooA, N-terminal domain                                                                          d1ft9b1 B:134-213       CO-sensing protein CooA, C-terminal domain               SCOP domains
               CATH domains 1ft9B01 B:2-132 Jelly Rolls                                                                                                        1ft9B02 B:133-212 '      winged helix' repressor DNA binding domain             - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.................................................................................hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....------...ee..hhhhhhhhhh.hhhhhhhhhhhhhhh...ee.....ee..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ft9 B   2 PPRFNIANVLLSPDGETFFRGFRSKIHAKGSLVCTGEGDENGVFVVVDGRLRVYLVGEEREISLFYLTSGDMFCMHSGCLVEATERTEVRFADIRTFEQKLQTCPSMAWGLIAILGRALTSCMRTIEDLMFHDIKQRIAGFFIDHANTTG------VIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQGRGHYTIPNLVRLKAAA 213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      |161       171       181       191       201       211  
                                                                                                                                                                               151    158
   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)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FT9)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P72322_RHORU | P72322)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ft9)
 

(-) 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
  1ft9
    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
  P72322_RHORU | P72322
    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
  P72322_RHORU | P72322
    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 1FT9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1FT9)