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
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
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)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE T. VAGINALIS IBP39 INITIATOR BINDING DOMAIN (IBD) BOUND TO THE ALPHA-SCS INR ELEMENT
 
Authors :  M. A. Schumacher, A. O. T. Lau, P. J. Johnson
Date :  16 Jun 03  (Deposition) - 18 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym. Unit :  E,F,G,I,J,K,M,O,P,R,T,U,V,Y
Biol. Unit 1:  F,J,K  (1x)
Biol. Unit 2:  M,R,Y  (1x)
Biol. Unit 3:  E,G,U  (1x)
Biol. Unit 4:  I,P,T  (1x)
Biol. Unit 5:  V  (1x)
Biol. Unit 6:  O  (1x)
Keywords :  Ibp39, Initiator Binding Protein, Inr, Core Promoter, Transcription, T. Vaginalis, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, A. O. T. Lau, P. J. Johnson
Structural Basis Of Core Promoter Recognition In A Primitive Eukaryote
Cell(Cambridge, Mass. ) V. 115 413 2003
PubMed-ID: 14622596  |  Reference-DOI: 10.1016/S0092-8674(03)00887-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-SCS INR
    Chains: E, I, Y, K
    Engineered: YES
    Other Details: THE ALPHA-SCS INR PROMOTER ELEMENT, DNA SITE
    Synthetic: YES
 
Molecule 2 - ALPHA-SCS INR
    Chains: T, R, J, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 39 KDA INITIATOR BINDING PROTEIN
    Chains: U, P, F, V, M, O
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEQ60
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-126
    Organism Scientific: TRICHOMONAS VAGINALIS
    Organism Taxid: 5722

 Structural Features

(-) Chains, Units

  1234567891011121314
Asymmetric Unit : EFGIJKMOPRTUVY
Biological Unit 1 (1x):  F  JK        
Biological Unit 2 (1x):       M  R   Y
Biological Unit 3 (1x): E G        U  
Biological Unit 4 (1x):    I    P T   
Biological Unit 5 (1x):             V 
Biological Unit 6 (1x):        O      

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS V:69 , ASN V:84 , HIS V:97BINDING SITE FOR RESIDUE SO4 V 599
2AC2SOFTWARELYS O:69 , LEU O:80 , ASN O:84 , HIS O:97BINDING SITE FOR RESIDUE SO4 O 299

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PP8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PP8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PP8)

(-) Exons   (0, 0)

(no "Exon" information available for 1PP8)

(-) 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 E from PDB  Type:DNA  Length:12
                                            
                 1pp8 E  26 GTCACTTCACAT  37
                                    35  


Chain F from PDB  Type:PROTEIN  Length:113
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:113
                                    11        21        31        41        51        61        71        81        91       101       111   
         Q95VR4_TRIVA     2 DSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNS 114
               SCOP domains d1pp8f_ F: 39 kda initiator binding protein, IBP39, N-terminal domain                                             SCOP domains
               CATH domains 1pp8F00 F:2-114 'winged helix' repressor DNA binding domain                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhheee.....eeehhhhhhhhh..hhhhhhhhhhhh..ee.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1pp8 F   2 DSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNS 114
                                    11        21        31        41        51        61        71        81        91       101       111   


Chain G from PDB  Type:DNA  Length:12
                                            
                 1pp8 G   3 CATGTGAAGTGA  14
                                    12  


Chain I from PDB  Type:DNA  Length:12
                                            
                 1pp8 I  26 GTCACTTCACAT  37
                                    35  


Chain J from PDB  Type:DNA  Length:12
                                            
                 1pp8 J   3 CATGTGAAGTGA  14
                                    12  


Chain K from PDB  Type:DNA  Length:12
                                            
                 1pp8 K  26 GTCACTTCACAT  37
                                    35  


Chain M from PDB  Type:PROTEIN  Length:118
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
         Q95VR4_TRIVA     1 MDSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSVFED 118
               SCOP domains d1pp8m_ M: 39 kda initiator binding protein, IBP39, N-terminal domain                                                  SCOP domains
               CATH domains 1pp8M00 M:1-118 'winged helix' repressor DNA binding domain                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhheee.....eeeehhhhhhhh..hhhhhhhhhhhh..eeee.............ee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1pp8 M   1 MDSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSVFED 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain O from PDB  Type:PROTEIN  Length:97
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:106
                                    19        29        39        49        59        69        79        89        99       109      
         Q95VR4_TRIVA    10 FTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSV 115
               SCOP domains d1pp8o_ O: 39 k         da initiator binding protein, IBP39, N-terminal domain                             SCOP domains
               CATH domains 1pp8O00 O:10-11         5 'winged helix' repressor DNA binding domain                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh---------.hhhhhhhhhhhh.hhhhhhhhheee....eeeehhhhhhhhhh..hhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1pp8 O  10 FTSRLPPEIVAALKR---------FPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSV 115
                                    19    |    -    |   39        49        59        69        79        89        99       109      
                                         24        34                                                                                 


Chain P from PDB  Type:PROTEIN  Length:118
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:118
                                    10        20        30        40        50        60        70        80        90       100       110        
         Q95VR4_TRIVA     1 MDSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSVFED 118
               SCOP domains d1pp8p_ P: 39 kda initiator binding protein, IBP39, N-terminal domain                                                  SCOP domains
               CATH domains 1pp8P00 P:1-118 'winged helix' repressor DNA binding domain                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhheee.....eeehhhhhhhhh..hhhhhhhhhhhh.............ee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1pp8 P   1 MDSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSVFED 118
                                    10        20        30        40        50        60        70        80        90       100       110        


Chain R from PDB  Type:DNA  Length:12
                                            
                 1pp8 R   3 CATGTGAAGTGA  14
                                    12  


Chain T from PDB  Type:DNA  Length:12
                                            
                 1pp8 T   3 CATGTGAAGTGA  14
                                    12  


Chain U from PDB  Type:PROTEIN  Length:111
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:111
                                    11        21        31        41        51        61        71        81        91       101       111 
         Q95VR4_TRIVA     2 DSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTR 112
               SCOP domains d1pp8u_ U: 39 kda initiator binding protein, IBP39, N-terminal domain                                           SCOP domains
               CATH domains 1pp8U00 U:2-112 'winged helix' repressor DNA binding domain                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.eee....eeeehhhhhhhhh..hhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1pp8 U   2 DSNDLEASFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTR 112
                                    11        21        31        41        51        61        71        81        91       101       111 


Chain V from PDB  Type:PROTEIN  Length:98
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:107
                                    18        28        38        48        58        68        78        88        98       108       
         Q95VR4_TRIVA     9 SFTSRLPPEIVAALKRKSSRDPNSRFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSV 115
               SCOP domains d1pp8v_ V: 39 k         da initiator binding protein, IBP39, N-terminal domain                              SCOP domains
               CATH domains 1pp8V00 V:9-115          'winged helix' repressor DNA binding domain                                        CATH domains
           Pfam domains (1) IBD-1pp8V01 V:9         -112                                                                            --- Pfam domains (1)
           Pfam domains (2) IBD-1pp8V02 V:9         -112                                                                            --- Pfam domains (2)
           Pfam domains (3) IBD-1pp8V03 V:9         -112                                                                            --- Pfam domains (3)
           Pfam domains (4) IBD-1pp8V04 V:9         -112                                                                            --- Pfam domains (4)
           Pfam domains (5) IBD-1pp8V05 V:9         -112                                                                            --- Pfam domains (5)
           Pfam domains (6) IBD-1pp8V06 V:9         -112                                                                            --- Pfam domains (6)
         Sec.struct. author .hhhhhhhhhhhhh.---------.hhhhhhhhhhhhh...hhhhhh.eee....eeeehhhhhhhhhh.hhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1pp8 V   9 SFTSRLPPEIVAALK---------RFPRKLHMLLTYLASNPQLEEEIGLSWISDTEFKMKKKNVALVMGIKLNTLNVNLRDLAFEQLQHDKGGWTQWKRSGFTRNSV 115
                                    18    |    -    |   38        48        58        68        78        88        98       108       
                                         23        33                                                                                  


Chain Y from PDB  Type:DNA  Length:12
                                            
                 1pp8 Y  26 GTCACTTCACAT  37
                                    35
   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, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: IBD] (2)
(-)
Family: IBD (2)
(-)
Trichomonas vaginalis (2)
1aIBD-1pp8V01V:9-112
1bIBD-1pp8V02V:9-112
1cIBD-1pp8V03V:9-112
1dIBD-1pp8V04V:9-112
1eIBD-1pp8V05V:9-112
1fIBD-1pp8V06V:9-112

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1PP8)

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pp8)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ 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 | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 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
  1pp8
    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
  Q95VR4_TRIVA | Q95VR4
    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
  Q95VR4_TRIVA | Q95VR4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q95VR4_TRIVA | Q95VR4: 1pp7 1q87 1q88 1q89

(-) Related Entries Specified in the PDB File

1pp7 THE STRUCTURE OF THE IBD BOUND TO THE FERREDOXIN INR ELEMENT