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 :  STRUCTURAL BASIS FOR UTP SPECIFICITY OF RNA EDITING TUTASES FROM TRYPANOSOMA BRUCEI
 
Authors :  J. Deng, N. L. Ernst, S. Turley, K. D. Stuart, W. G. Hol
Date :  27 Sep 05  (Deposition) - 22 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Tbret2, Tutase, Rna Editing, Transferase, Trypanosoma Brucei, Transferase-Rna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Deng, N. L. Ernst, S. Turley, K. D. Stuart, W. G. Hol
Structural Basis For Utp Specificity Of Rna Editing Tutases From Trypanosoma Brucei.
Embo J. V. 24 4007 2005
PubMed-ID: 16281058  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600861

(-) Compounds

Molecule 1 - RNA EDITING COMPLEX PROTEIN MP57
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTA
    Expression System Strain: BL21 GOLD DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TBMP57
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2U5P2Ligand/IonURIDINE-5'-MONOPHOSPHATE
3UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:97 , ASP A:99 , UTP A:501 , HOH A:874BINDING SITE FOR RESIDUE MG A 488
2AC2SOFTWAREGLY A:84 , SER A:85 , SER A:96 , ASP A:97 , ASP A:99 , GLY A:274 , ASN A:277 , SER A:278 , LYS A:300 , LYS A:304 , SER A:318 , TYR A:319 , MG A:488 , HOH A:633 , HOH A:639 , HOH A:653 , HOH A:720 , HOH A:759 , HOH A:814 , HOH A:830 , HOH A:831 , HOH A:874BINDING SITE FOR RESIDUE UTP A 501
3AC3SOFTWAREARG A:144 , SER A:312 , GLY A:313 , ALA A:314 , MET A:315 , THR A:317 , ARG A:435 , HIS A:436 , HOH A:645 , HOH A:690 , HOH A:737 , HOH A:805BINDING SITE FOR RESIDUE U5P A 601
4AC4SOFTWAREARG A:282 , PRO A:350 , TYR A:352 , PRO A:353 , ASP A:354 , HOH A:677 , HOH A:682 , HOH A:768 , HOH A:774BINDING SITE FOR RESIDUE U5P A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B56)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:234 -Pro A:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B56)

(-) Exons   (0, 0)

(no "Exon" information available for 2B56)

(-) 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:444
 aligned with Q86MV5_9TRYP | Q86MV5 from UniProtKB/TrEMBL  Length:487

    Alignment length:444
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469    
         Q86MV5_9TRYP    30 NPSPDHYAVWGKAIMAENNRRVGPEHMFRTAIRAQQQLQGLADKWTPDAKVYCCGSMVTYGQMEWGSDLDLACMFDDPYPSHEVQAKRTDKLWTVIKRYVPHYLRNNLLGLTEARTPVVKLRFANDEKVARARYTPLSEEEDRKARTALLDVRNQCVGDNDVEYIAEKMGRDNVEGIWVDRTTYGCRIAIQCTSKEQMIEAIGFFPDGKIMTRGMREDYTRDVLDVRFVPEMFMYRWDISFVGYGVKNSYLIRHYLHNGPVAARHTAMAVKAWGKATNVGAGSGAMLTSYAVTVMFIYYLLVTRQVLWVDPWSLPHPAHLPRYPDFSPLYDCDPTELGRLLHGFFIFYAHHFDYEREVVSLNRNRRSYRSDIGWNFPQNKKGTFSYNFCIEDPYEDVGTGGLNLVRHLHPAKFQLVKQEFLRAAQCMERFLPTNAPEKSILGVK 473
               SCOP domains d2b56a1 A:30-288 RNA editing terminal uridyl transferase 2, TUTase 2, RET2                                                                                                                                                                                         d2b56a2 A:289-473 RNA editing terminal uridyl transferase 2, TUTase 2, RET2                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhh.......eeeeee......hhhhhhhhhhhhhhhhhh..hhhhhh.eeee......eeee...hhhhhhhhhhh..hhhhhhhhheeeeeee....hhhhhhhhhhhhh...eeeeeee....eeeeeeee.hhhhhhhhhh........hhhhhh.eeeee......hhhhh..eeee..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh......hhhhh.hhhhh............hhhhhhhhhhhhhhhhhhh.....ee........eehhhhh..hhh.ee..ee.......................hhhhhhhhhhhhhhhhhhhhhh.......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b56 A  30 NPSPDHYAVWGKAIMAENNRRVGPEHMFRTAIRAQQQLQGLADKWTPDAKVYCCGSMVTYGQMERGSDLDLACMFDDPYPSHEVQAKRTDKLRTVIKRYVPHYLRNNLLGLTEARTPVVKLRFANDEKVARARYTPLSEEEDRKARTALLDVRNQCVGDNDVEYIAEKMGRDNVEGIRVDRTTYGCRIAIQCTSKEQMIEAIGFFPDGKIMTRGMREDYTRDVLDVRFVPEMFMYRWDISFVGYGVKNSYLIRHYLHNGPVAARHTAMAVKAWGKATNVGAGSGAMLTSYAVTVMFIYYLLVTRQVLWVDPWSLPHPAHLPRYPDFSPLYDCDPTELGRLLHGFFIFYAHHFDYEREVVSLNRNRRSYRSDIGWNFPQNKKGTFSYNFCIEDPYEDVGTGGLNLVRHLHPAKFQLVKQEFLRAAQCMERFLPTNAPEKSILGVK 473
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B56)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2B56)

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    U5P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:234 - Pro A:235   [ 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
  2b56
    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
  Q86MV5_9TRYP | Q86MV5
    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
  Q86MV5_9TRYP | Q86MV5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q86MV5_9TRYP | Q86MV5: 2b4v 2b51

(-) Related Entries Specified in the PDB File

2b4v 2b51