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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-DOMAIN OF THE T.VAGINALIS INR BINDING PROTEIN, IBP39 (TETRAGONAL FORM)
 
Authors :  M. A. Schumacher, P. J. Johnson
Date :  20 Aug 03  (Deposition) - 18 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Initiator, Inr, Initiator Binding Protein, Core Promoter, Dna Binding Protein (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 - 39 KDA INITIATOR BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-DOMAIN, RESIDUES 127-341
    Gene: IBP39
    Organism Scientific: TRICHOMONAS VAGINALIS
    Organism Taxid: 5722

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Q87)

(-) Sites  (0, 0)

(no "Site" information available for 1Q87)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q87)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:212 -Pro A:213
2Gly A:232 -Pro A:233
3Ala B:212 -Pro B:213
4Gly B:232 -Pro B:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q87)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q87)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q87)

(-) 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:185
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:199
                                                                                                                                                                                                                            341    
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    |    
         Q95VR4_TRIVA   147 SMCIGNSTPNEQETFRAKVDEIWFRLTQKTDGTVMRDFLIEKAAEYFKQPEQPKQNAIEVISAIMAPQEEQTKSKADLYKFLAMFGPYETIMLKIASLLLISNNKGHWLTFDPQAEKNANNQRDSISGWFDQNEPNCLILKTPTGIRKIWNKPLIEATGQYLMDENGEKYDSWDKYFEMKPIETYLTAYPTFAPM----   -
               SCOP domains d1q87a_ A: 39 kda initiator binding protein, IBP39, C-terminal domains                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh....hhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........---------...eeeee..eeeeeeeee..eeeeeee..........ee.....ee.hhhhhhhhh..-----......hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q87 A 147 SMCIGNSTPNEQETFRAKVDEIWFRLTQKTDGTVMRDFLIEKAAEYFKQPEQPKQNAIEVISAIMAPQEEQTKSKADLYKFLAMFGPYETIMLKIASLLLISNNKGHWLTFDPQ---------DSISGWFDQNEPNCLILKTPTGIRKIWNKPLIEATGQYLMDENGEKYDSWDKYFEMKPI-----AYPTFAPMHHHH 345
                                   156       166       176       186       196       206       216       226       236       246       256   |     -   |   276       286       296       306       316       326 |     336         
                                                                                                                                           260       270                                                       328   334           


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with Q95VR4_TRIVA | Q95VR4 from UniProtKB/TrEMBL  Length:341

    Alignment length:198
                                                                                                                                                                                                                            341   
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336    |   
         Q95VR4_TRIVA   147 SMCIGNSTPNEQETFRAKVDEIWFRLTQKTDGTVMRDFLIEKAAEYFKQPEQPKQNAIEVISAIMAPQEEQTKSKADLYKFLAMFGPYETIMLKIASLLLISNNKGHWLTFDPQAEKNANNQRDSISGWFDQNEPNCLILKTPTGIRKIWNKPLIEATGQYLMDENGEKYDSWDKYFEMKPIETYLTAYPTFAPM---   -
               SCOP domains d1q87b_ B: 39 kda initiator binding protein, IBP39, C-terminal domains                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) IBP39-1q87B01 B:147-326                                                                                                                                                             ------------------ Pfam domains (1)
           Pfam domains (2) IBP39-1q87B02 B:147-326                                                                                                                                                             ------------------ Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhh....hhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............-----..eeee......eeeeee..eeeeeee..........ee.....ee.hhhhhhhhh.............hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q87 B 147 SMCIGNSTPNEQETFRAKVDEIWFRLTQKTDGTVMRDFLIEKAAEYFKQPEQPKQNAIEVISAIMAPQEEQTKSKADLYKFLAMFGPYETIMLKIASLLLISNNKGHWLTFDPQAEKNA-----SISGWFDQNEPNCLILKTPTGIRKIWNKPLIEATGQYLMDENGEKYDSWDKYFEMKPIETYLTAYPTFAPMHHH 344
                                   156       166       176       186       196       206       216       226       236       246       256        |-    |  276       286       296       306       316       326       336        
                                                                                                                                                265   271
   Legend:   → Mismatch (orange background)
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  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, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Q87)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: IBP39] (3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Q87)

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  Sites
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  Cis Peptide Bonds
    Ala A:212 - Pro A:213   [ RasMol ]  
    Ala B:212 - Pro B:213   [ RasMol ]  
    Gly A:232 - Pro A:233   [ RasMol ]  
    Gly B:232 - Pro B:233   [ RasMol ]  
 
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  1q87
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 Related Entries

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

UniProtKB/TrEMBL
        Q95VR4_TRIVA | Q95VR4: 1pp7 1pp8 1q88 1q89

(-) Related Entries Specified in the PDB File

1pp7
1pp8
1q88 C-DOMAIN (MONOCLINIC CRYSTAL FORM)
1q89 C-DOMAIN (CUBIC CRYSTAL FORM)