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(-) Description

Title :  STRUCTURE OF RAD14 IN COMPLEX WITH ACETYLNAPHTYL-GUANINE CONTAINING DNA
 
Authors :  N. Simon, C. Ebert, S. Schneider
Date :  18 Apr 16  (Deposition) - 01 Jun 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Cell Cycle, Dna Repair, Nucleotide Excision Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Schneider, N. Simon, C. Ebert
Structural Basis For Bulky Adduct Dna Lesion Recognition By The Nucleotide Excision Repair Protein Rad14.
Chemistry V. 22 10782 2016
PubMed-ID: 27223336  |  Reference-DOI: 10.1002/CHEM.201602438

(-) Compounds

Molecule 1 - RAD14
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 188-306
    Gene: RAD14, YMR201C, YM8325.02C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - 5'-D(*GP*CP*TP*CP*TP*AP*MFOP*TP*CP*AP*TP*CP*AP*CP)-3'
    Chains: C, E
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
 
Molecule 3 - 5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
    Chains: D, F
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MFO2Mod. Nucleotide[(2~{R},3~{S},5~{R})-5-[2-AZANYL-8-[ETHANOYL(NAPHTHALEN-2-YL)AMINO]-6-OXIDANYLIDENE-3~{H}PURIN-9-YL]-3-OXIDANYL-OXOLAN-2-YL]METHYLDIHYDROGEN PHOSPHATE
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 388
2AC2SOFTWARECYS B:191 , CYS B:194 , CYS B:213 , CYS B:216 , ARG B:264BINDING SITE FOR RESIDUE ZN B 388

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5G33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G33)

(-) Exons   (0, 0)

(no "Exon" information available for 5G33)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhh.....hhhhhhhhhhhhheeehhhhhhhhh.hhhhhh.......eee..........eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5g33 A 188 APKCIECHINIEMDPVLHDVFKLQVCKQCSKEHPEKYALLTKTECKEDYFLTDPELNDEDLFHRLEKPNPHSGTFARMQLFVRCEVEAFAFKKWGGEEGLDEEWQRREEGKAHR 301
                                   197       207       217       227       237       247       257       267       277       287       297    


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhh.....hhhhhhhhhhhhheeehhhhhhhhh.hhhhhhh......eee..........eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 5g33 B 188 APKCIECHINIEMDPVLHDVFKLQVCKQCSKEHPEKYALLTKTECKEDYFLTDPELNDEDLFHRLEKPNPHSGTFARMQLFVRCEVEAFAFKKWGGEEGLDEEWQRREEGKAHRR 302
                                   197       207       217       227       237       247       257       267       277       287       297     


Chain C from PDB  Type:DNA  Length:14
                                              
                 5g33 C   1 GCTCTACxTCATCA  14
                                   |10    
                                   8-MFO  


Chain D from PDB  Type:DNA  Length:14
                                              
                 5g33 D   1 GTGATGACGTAGAG  14
                                    10    


Chain E from PDB  Type:DNA  Length:14
                                              
                 5g33 E   1 GCTCTACxTCATCA  14
                                   |10    
                                   8-MFO  


Chain F from PDB  Type:DNA  Length:14
                                              
                 5g33 F   1 GTGATGACGTAGAG  14
                                    10
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  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 5G33)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G33)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G33)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  5g33
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5g32 STRUCTURE OF RAD14 IN COMPLEX WITH ACETYLPHENYL-GUANINE CONTAINING DNA
5g34 STRUCTURE OF RAD14 IN COMPLEX WITH ACETYLAMINOANTHRACENE- C8-GUANINE CONTAINING DNA
5g35 STRUCTURE OF RAD14 IN COMPLEX WITH ACETYLAMINOPYREN-C8- GUANINE CONTAINING DNA