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(-) Description

Title :  STRUCTURE OF THE RAD14 DNA-BINDING DOMAIN IN COMPLEX WITH N2-ACETYLAMINONAPHTYL- GUANINE CONTAINING DNA
 
Authors :  S. Schneider, C. Ebert, N. Simon, T. Carell
Date :  22 Jun 16  (Deposition) - 10 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nucleotide Excision Repair Dna Damage Recognition, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ebert, N. Simon, S. Schneider, T. Carell
Structural Insights Into The Recognition Of N(2) -Aryl- And C8-Aryl Dna Lesions By The Repair Protein Xpa/Rad14.
Chembiochem 2017
PubMed-ID: 28444956  |  Reference-DOI: 10.1002/CBIC.201700169

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RAD14
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Gene: RAD14, YMR201C, YM8325.02C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
 
Molecule 2 - DNA (5'-D(*GP*CP*TP*CP*TP*AP*CP*(AAN)P*TP*CP*AP*TP*CP*A)- 3')
    Chains: C
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
16TW1Mod. Nucleotide[(2~{R},3~{S},5~{R})-5-[2-[(3-ACETAMIDONAPHTHALEN-2-YL)AMINO]-6-OXIDANYLIDENE-1~{H}-PURIN-9-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHITE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:191 , CYS A:194 , CYS A:213 , CYS A:216 , ARG A:264binding site for residue ZN A 401
2AC2SOFTWARECYS B:191 , CYS B:194 , CYS B:213 , CYS B:216 , ARG B:264binding site for residue ZN B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LCM)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhh.....hhhhhhhhhhhhheeehhhhhhhhh.hhhhhh.......eee..........eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 5lcm A 188 APKCIECHINIEMDPVLHDVFKLQVCKQCSKEHPEKYALLTKTECKEDYFLTDPELNDEDLFHRLEKPNPHSGTFARMQLFVRCEVEAFAFKKWGGEEGLDEEWQRREEGKAHRR 302
                                   197       207       217       227       237       247       257       267       277       287       297     


Chain B from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhh.....hhhhhhhhhhhhheeehhhhhhhhh.hhhhhh.......eee..........eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5lcm B 188 APKCIECHINIEMDPVLHDVFKLQVCKQCSKEHPEKYALLTKTECKEDYFLTDPELNDEDLFHRLEKPNPHSGTFARMQLFVRCEVEAFAFKKWGGEEGLDEEWQRREEGKAHR 301
                                   197       207       217       227       237       247       257       267       277       287       297    


Chain C from PDB  Type:DNA  Length:14
                                              
                 5lcm C   1 GCTCTACxTCATCA  14
                                   |10    
                                   8-6TW  


Chain D from PDB  Type:DNA  Length:14
                                              
                 5lcm D   1 GTGATGACGTAGAG  14
                                    10
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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 5LCM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        RAD14_YEAST | P28519: 5a39 5a3d 5g32 5g33 5g34 5g35 5lcl

(-) Related Entries Specified in the PDB File

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