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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ENDOG WORM HOMOLOGUE CPS-6 H148A/F122A IN COMPLEX WITH DNA
 
Authors :  J. L. Lin, H. S. Yuan
Date :  05 Jul 16  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Endog, Mitochondria, Endonuclease, Non-Specific Nuclease, Protein-Dna Interactions, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Lin, C. C. Wu, W. Z. Yang, H. S. Yuan
Crystal Structure Of Endonuclease G In Complex With Dna Reveals How It Nonspecifically Degrades Dna As A Homodimer.
Nucleic Acids Res. 2016
PubMed-ID: 27738134  |  Reference-DOI: 10.1093/NAR/GKW931
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDONUCLEASE G, MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.1.30.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 63-305
    Gene: CPS-6, C41D11.8
    Mutation: YES
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: ENDO G,CED-3 PROTEASE SUPPRESSOR 6
 
Molecule 2 - DNA (5'-D(*TP*TP*TP*TP*T)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:180 , HOH A:505 , HOH A:530 , HOH A:532 , DT C:-1 , DT C:-2binding site for residue MG A 401
2AC2SOFTWAREASN B:180 , HOH B:513 , HOH B:516 , HOH B:566 , DT D:-2 , DT D:-1binding site for residue MG B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GKP)

(-) 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:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.........eee...eeeeee....eeeeeeeee.....................hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh....eeeeeeee..eee.....eeeeeeee....ee...eeeeeeeee.....eeeeeeeee........hhhhhh.hhhhhhhhhh.......hhh.eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkp A  64 SRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKGVDRKLCEAKPDITFPQKFLSQNTDYKCSGFDRGALAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGA 301
                                    73        83        93       103      |116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296     
                                                                        110|                                                                                                                                                                                           
                                                                         114                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.........eee....eeeee....eeeeeeeee.hhhhh..................hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh...eeeeeeeee..eee.....eeeeeeee....ee...eeeeeeeeeee..eeeeeeeeee.......hhhhhh.hhhhhhhhhh.......hhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkp B  63 PSRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAEGVDRKLCEAKPDITFPQKFLSQNTDYKCSGFDRGALAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIETVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK 302
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262||     273       283       293         
                                                                                                                                                                                                                                  263|                                     
                                                                                                                                                                                                                                   265                                     


Chain C from PDB  Type:DNA  Length:5
                                     
                 5gkp C  -3 TTTTT   1


Chain D from PDB  Type:DNA  Length:5
                                     
                 5gkp D  -3 TTTTT   1
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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 5GKP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        NUCG_CAEEL | Q95NM6: 3s5b 4qn0 5gkc

(-) Related Entries Specified in the PDB File

5gkc