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 :  RNA EDITING TUTASE 1 FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH UTP
 
Authors :  S. Thore, L. T. Rajappa
Date :  24 Feb 16  (Deposition) - 26 Oct 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Rna Editing Tutase1, Transferase, Trypanosoma Brucei (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Rajappa-Titu, T. Suematsu, P. Munoz-Tello, M. Long, O. Demir, K. J. Cheng, J. R. Stagno, H. Luecke, R. E. Amaro, I. Aphasizheva, R. Aphasizhev, S. Thore
Rna Editing Tutase 1: Structural Foundation Of Substrate Recognition, Complex Interactions And Drug Targeting.
Nucleic Acids Res. V. 44 10862 2016
PubMed-ID: 27744351  |  Reference-DOI: 10.1093/NAR/GKW917

(-) Compounds

Molecule 1 - 3' TERMINAL URIDYLYL TRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 189-699
    Gene: 3' TUTASE
    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, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2UTP1Ligand/IonURIDINE 5'-TRIPHOSPHATE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:479 , GLY A:480 , ASN A:483 , SER A:484 , LYS A:505 , LYS A:509 , SER A:523 , TYR A:524 , MG A:703 , HOH A:895 , HOH A:902 , HOH A:936binding site for residue UTP A 701
2AC2SOFTWARECYS A:195 , CYS A:198 , HIS A:212 , HIS A:217binding site for residue ZN A 702
3AC3SOFTWAREUTP A:701 , HOH A:936 , HOH A:949 , HOH A:952binding site for residue MG A 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IDO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:326 -Pro A:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IDO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IDO)

(-) Exons   (0, 0)

(no "Exon" information available for 5IDO)

(-) 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:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhh.......eeeeeeehhhhhhh....hhhhhhhhhhhhhhhh......eeee......eeee.....hhhh.eeeeee....hhhhhhhhhhhhhhhhh...eeeeee.....eeeeee.hhhhhhhhhh...........eeeee......hhhhhh.eeee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhh......hhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhh.....ee........ee.hhhh..............................hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ido A 190 VRLYSCDACPHAVFTTHAALLAHAEEHHADLLPDHARLRRIAQKLNPVWNRALNARRNTITSWGKKIFHVAAQRDAGESKMQEAHRARAQLECVVRRWHDKARVFIFGSSVAMGVWDGTADIDFAVVDVDAMERGSWPPLEKNAVRSITELLRRVGFSFVNLEPISHARVPIIKHHASSPDVVARSIRFILNGPATREDRLLLEGSVRDAVGPTGVQQVWWNRTSDMMSATLESTTAAVRAAMCSPALASASLRTKVQPAHDECRPELYNIDFALSFRAFGIRNSTLLRKYLLSHPCARPGAIVLKDWSKTSGVNNSVNGYFTSYAINIMWIYYLVQKGYVPYVDPLEIPESLVNYTDFDPRYTPMIDPEITNTEREELYKAAGDMLVGFFYFYSFEFDWGHNVISLNRPGITTKRMLGWHVEDVVHPTRYELCIEDPYEENLNLGRHIGVTKSLRVRTELYRGLLSLLKE 688
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369|      389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619     ||647       657       667       677       687 
                                                                                                                                                                                                             369|                                                                                                                                                                                                                                                  625|                                            
                                                                                                                                                                                                              380                                                                                                                                                                                                                                                   644
   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 5IDO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IDO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IDO)

(-) Gene Ontology  (1, 1)

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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:326 - Pro A:327   [ 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
  5ido
    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
  Q8WQX5_9TRYP | Q8WQX5
    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
  Q8WQX5_9TRYP | Q8WQX5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8WQX5_9TRYP | Q8WQX5: 5hzd 5i49

(-) Related Entries Specified in the PDB File

5i49 THIS IS THE SAME PROTEIN AS 5I49, EXCEPT THAT IT IS A CATALYTICALLY DEAD MUTANT D473A COMPLEXED WITH UTP IN THE ACTIVE SITE.