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 THERMUS THERMOPHILUS CATABOLITE ACTIVATOR PROTEIN
 
Authors :  B. P. Hudson, K. Turo, J. J. Birktoft, C. L. Lawson
Date :  25 Apr 12  (Deposition) - 20 Jun 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Camp Binding, Winged Helix-Turn-Helix Motif, Dna Binding, Transcription Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. P. Hudson, K. Turo, J. J. Birktoft, R. H. Ebright, C. L. Lawson
Crystal Structure Of T. Thermophilius Catabolite Activator Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTION REGULATOR, CRP FAMILY
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-TTCRP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CRP, TTHA1437
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8 / ATCC 27634 / DSM 579

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3SO45Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:34 , LEU A:53 , LEU A:65 , PHE A:74 , GLY A:75 , GLU A:76 , MET A:77 , SER A:78 , ARG A:85 , SER A:86 , ALA A:87 , ARG A:126 , HOH A:437BINDING SITE FOR RESIDUE CMP A 301
2AC2SOFTWARESER A:20 , TYR A:21 , GLN A:23 , ASP A:104 , ARG A:165 , HIS A:167 , MG A:304 , HOH A:421BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREHIS A:166 , HIS A:167 , ARG A:177 , HOH A:416BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREGLU A:103 , ASP A:104 , SO4 A:302BINDING SITE FOR RESIDUE MG A 304
5AC5SOFTWAREASP A:131 , PHE D:34 , LEU D:65 , PHE D:74 , GLY D:75 , GLU D:76 , MET D:77 , SER D:78 , ARG D:85 , SER D:86 , ALA D:87 , ARG D:126BINDING SITE FOR RESIDUE CMP D 301
6AC6SOFTWAREARG A:110 , LEU D:10 , GLU D:14 , LEU D:112 , PRO D:113 , LEU D:114 , HOH D:409BINDING SITE FOR RESIDUE SO4 D 302
7AC7SOFTWAREALA A:216 , ARG D:165 , HIS D:166 , HOH D:423 , HOH D:434BINDING SITE FOR RESIDUE SO4 D 303
8AC8SOFTWAREARG A:182 , HIS D:57 , LEU D:58BINDING SITE FOR RESIDUE SO4 D 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EV0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:159 -Pro A:160
2Gly D:159 -Pro D:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EV0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EV0)

(-) Exons   (0, 0)

(no "Exon" information available for 4EV0)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..hhhhhhhhhh..eeeee....eee.......eeeeeee..eeeeee.....eeeeeee....eehhhhhhhh.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ev0 A   4 SPLFHGLAPEEVDLALSYFQRRLYPQGKPIFYQGDLGQALYLVASGKVRLFRTHLGGQERTLALLGPGELFGEMSLLDEGERSASAVAVEDTELLALFREDYLALIRRLPLVAHNLAALLARRLREADLELDLLSFEEARNRVAYALLKLLRQGLGPLFQIRHHELAALAGTSRETVSRVLHALAEEGVVRLGPGTVEVREAALLEEIAFGLA 216
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   


Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhh..eeeee....eee.......eeeeeee..eeeeeee...eeeeeeee....eehhhhhhhh.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ev0 D   3 GSPLFHGLAPEEVDLALSYFQRRLYPQGKPIFYQGDLGQALYLVASGKVRLFRTHLGGQERTLALLGPGELFGEMSLLDEGERSASAVAVEDTELLALFREDYLALIRRLPLVAHNLAALLARRLREADLELDLLSFEEARNRVAYALLKLLRQGLGPLFQIRHHELAALAGTSRETVSRVLHALAEEGVVRLGPGTVEVREAALLEEIAFGLA 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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 4EV0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EV0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EV0)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
    Gly A:159 - Pro A:160   [ RasMol ]  
    Gly D:159 - Pro D:160   [ RasMol ]  
 

(-) 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
  4ev0
    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
  CRP_THET8 | Q5SID7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  CRP_THET8 | Q5SID7
    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 4EV0)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4EV0)