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(-) Description

Title :  CRYSTAL STRUCTURE OF LEISHMANIA INFANTUM POLYMERASE BETA: NICK 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,B,C,D
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*CP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*CP*CP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(P*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:100 , VAL A:102 , PHE A:105 , HOH A:646 , DA C:5 , HOH C:117binding site for residue NA A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P4P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:289 -Ser A:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P4P)

(-) Exons   (0, 0)

(no "Exon" information available for 4P4P)

(-) 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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeeehhhhhh...ee..eeeeeee.........hhhhhhhhhhhhhhhhhh..eeeeeee...eeeeee.............eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee..hhhhhhhhhhhhh.......ee..eehhhhhh......hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p4p A  32 KYKVPKLKAIQELTQVHGFGPRAAAALFDREGIFTVDELLQKADSIPSLTDQQRVGIKYFYDINEKIPMQESVLHENYLREKCMEVLGKDFSILICGSYRRRHPFSGDVDAILSRTLDAPPLSEPVAATGVLGHFVEFLESLKYLEATMAQGPLKYMGMGRLPPRINTKVYKARRVDIRLIETKSVPTAMLTFTGSKNFNVIMRQAAISKGYLLNEYGLFKLGTPEEARALYERIGIRGKNAGEELGVPKDELEDKRVEVRSEQDVFDVLGMPYAKPENRDP 376
                               ||   96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246     ||264       274       284       294       304       314       324       334       344       354       364       374  
                              35|                                                                                                                                                              252|                                                                                                                   
                               91                                                                                                                                                               261                                                                                                                   


Chain B from PDB  Type:DNA  Length:10
                                          
                 4p4p B   2 GGCAGTACTG  11
                                    11


Chain C from PDB  Type:DNA  Length:7
                                       
                 4p4p C   1 CAGTACT   7


Chain D from PDB  Type:DNA  Length:2
                                  
                 4p4p D   1 GC   2
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  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 4P4P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P4P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P4P)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:289 - Ser A:290   [ RasMol ]  
 

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