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(-)Asym./Biol. Unit
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(-) Description

Title :  ALKYLPURINE DNA GLYCOSYLASE ALKD BOUND TO DNA CONTAINING A 3-METHYLADENINE ANALOG (9-MER A)
 
Authors :  E. A. Mullins, B. F. Eichman
Date :  16 Jul 15  (Deposition) - 28 Oct 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Glycosylase, Heat-Like Repeat, Protein-Dna Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Mullins, R. Shi, Z. D. Parsons, P. K. Yuen, S. S. David, Y. Igarashi B. F. Eichman
The Dna Glycosylase Alkd Uses A Non-Base-Flipping Mechanism To Excise Bulky Lesions.
Nature V. 527 254 2015
PubMed-ID: 26524531  |  Reference-DOI: 10.1038/NATURE15728

(-) Compounds

Molecule 1 - ALKD
    Atcc: 14579
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBG103
    Expression System Strain: HMS174
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IKE_03968
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
 
Molecule 2 - DNA (5'-D(*AP*AP*GP*CP*AP*(DZM)P*AP*CP*C)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*GP*GP*TP*TP*TP*GP*CP*T)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DZM1Mod. Nucleotide3-DEAZA-3-METHYLADENINE

(-) Sites  (0, 0)

(no "Site" information available for 5CLB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CLB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CLB)

(-) 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    
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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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5clb A  -1 VPMHPFVKALQEHFTAHQNPEKAEPMARYMKNHFLFLGIQTPERRQLLKDIIQLPDQKDFQIIIRELWDLPEREFQAAALDIMQKYKKHINETHIPFLEELIVTKSWWDSVDSIVPTFLGDIFLKHPELISAYIPKWIASDNIWLQRAAILFQLKYKQKMDEELLFWIIGQLHSSKEFFIQKAIGWVLREYAKTNPDVVWEYVQNNELAPLSKREAIKHIKQNY 225
                                     8        18        28        38        48  ||    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
                                                                               51|                                                                                                                                                                          
                                                                                55                                                                                                                                                                          


Chain B from PDB  Type:DNA  Length:9
                                         
                 5clb B   1 AAGCAxACC   9
                                 |   
                                 6-DZM


Chain C from PDB  Type:DNA  Length:9
                                         
                 5clb C  10 TGGTTTGCT  18
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5CLB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

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

UniProtKB/Swiss-Prot
        R8GWR7_BACCE | R8GWR7: 5cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cl9 5cla 5clc 5cld 5cle
UniProtKB/TrEMBL
        Q816E8_BACCR | Q816E8: 3bvs 3jx7 3jxy 3jxz 3jy1 5cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cl9 5cla 5clc 5cld 5cle 5kub

(-) Related Entries Specified in the PDB File

5cl3 5cl4 5cl5 5cl6 5cl7 5cl8 5cl9 5cla 5clc 5cld 5cle