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 LEISHMANIA INFANTUM POLYMERASE BETA: TERNARY GAP COMPLEX
 
Authors :  E. Mejia, M. Burak, A. Alonso, V. Larraga, T. Kunkel, K. Bebenek, M. Garc
Date :  12 Mar 14  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,E,F,G
Keywords :  Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Mejia, M. Burak, A. Alonso, V. Larraga, T. A. Kunkel, K. Bebenek, M. Garcia-Diaz
Structures Of The Leishmania Infantum Polymerase Beta.
Dna Repair (Amst. ) V. 18 1 2014
PubMed-ID: 24666693  |  Reference-DOI: 10.1016/J.DNAREP.2014.03.001

(-) Compounds

Molecule 1 - DNA POLYMERASE BETA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LEISHMANIA INFANTUM
    Organism Taxid: 5671
 
Molecule 2 - DNA (5'-D(*CP*AP*GP*TP*AP*T)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*CP*CP*G)-3')
    Chains: G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3')
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : AEFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1D3T1Ligand/Ion2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:183 , SER A:184 , ARG A:187 , SER A:192 , GLY A:193 , ASP A:194 , ASP A:196 , THR A:286 , PHE A:287 , LYS A:291 , ASN A:294 , MG A:403 , HOH A:586 , HOH A:615 , HOH A:624 , HOH A:702 , HOH A:703 , DT E:6 , DA F:5binding site for residue D3T A 401
2AC2SOFTWARETHR A:100 , VAL A:102 , PHE A:105 , DA E:5binding site for residue NA A 402
3AC3SOFTWAREASP A:194 , ASP A:196 , D3T A:401 , HOH A:578binding site for residue MG A 403
4AC4SOFTWAREHOH A:508 , HOH A:509 , DT F:10 , HOH F:205 , HOH F:209 , HOH F:213binding site for residue NA F 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P4O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:69 -Leu A:70
2Gly A:289 -Ser A:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P4O)

(-) Exons   (0, 0)

(no "Exon" information available for 4P4O)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhh..eeeeehhhhhh...ee..eeeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeee...eeeeee.............eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee..hhhhhhhhhhhh........ee..eehhhhhh.ee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p4o A  20 QEMADLNNALGEKYKVSSYHKLLKKATKPKLKAIQELTQVHGFGPRAAAALFDREGIFTVDELLQKADSIPSLTDQQRVGIKYFYDINEKIPMQESVLHENYLREKCMEVLGKDFSILICGSYRRRHPFSGDVDAILSRTLDAPPLSEPVAATGVLGHFVEFLESLKYLEATMAQGPLKYMGMGRLPPRINTKVYKARRVDIRLIETKSVPTAMLTFTGSKNFNVIMRQAAISKGYLLNEYGLFKLGTPEEARALYERIGIRGKNAGEELGVPKDELEDKRVEVRSEQDVFDVLGMPYAKPENRDP 376
                                    29        39|    || 92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252|      270       280       290       300       310       320       330       340       350       360       370      
                                              39|   73|                                                                                                                                                                252|                                                                                                                   
                                               68    89                                                                                                                                                                 261                                                                                                                   


Chain E from PDB  Type:DNA  Length:6
                                      
                 4p4o E   1 CAGTAT   6


Chain F from PDB  Type:DNA  Length:10
                                          
                 4p4o F   2 GGCAATACTG  11
                                    11


Chain G from PDB  Type:DNA  Length:3
                                   
                 4p4o G   1 GCC   3
   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 4P4O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P4O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P4O)

(-) Gene Ontology  (6, 6)

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
    D3T  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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
    Gly A:289 - Ser A:290   [ RasMol ]  
    Leu A:69 - Leu A:70   [ 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
  4p4o
    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
  Q9U6N3_LEIIN | Q9U6N3
    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
  Q9U6N3_LEIIN | Q9U6N3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9U6N3_LEIIN | Q9U6N3: 4p4m 4p4p

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4P4O)