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(-) Description

Title :  STRUCTURE OF ENDOMS-DSDNA2 COMPLEX
 
Authors :  S. Nakae, A. Hijikata, T. Tsuji, K. Yonezawa, K. Kouyama, K. Mayanagi, S Y. Ishino, T. Shirai
Date :  04 Jul 16  (Deposition) - 02 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Endonuclease, Dna-Complex, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nakae, A. Hijikata, T. Tsuji, K. Yonezawa, K. I. Kouyama, K. Mayanagi, S. Ishino, Y. Ishino, T. Shirai
Structure Of The Endoms-Dna Complex As Mismatch Restriction Endonuclease
Structure V. 24 1960 2016
PubMed-ID: 27773688  |  Reference-DOI: 10.1016/J.STR.2016.09.005

(-) Compounds

Molecule 1 - ENDONUCLEASE ENDOMS
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TK1898
    Mutation: YES
    Organism Scientific: THERMOCOCCUS KODAKARENSIS KOD1
    Organism Taxid: 69014
    Strain: KOD1
    Synonym: ENDONUCLEASE NUCS
 
Molecule 2 - DNA (5'-D(*CP*GP*TP*GP*CP*CP*AP*GP*GP*TP*GP*CP*CP*GP*T)- 3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*CP*GP*GP*CP*AP*CP*TP*TP*GP*GP*CP*AP*CP*G)- 3')
    Chains: D
    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  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:10 , SER A:11 , GLU A:16 , ASP B:172binding site for residue MPD A 301
2AC2SOFTWAREILE A:163 , GLU A:179 , GLN A:192 , DC C:5 , DC C:6 , DC D:5 , DA D:6binding site for residue MG A 302
3AC3SOFTWAREGLU B:132 , GLU B:179 , DC C:5 , DC C:6 , DC D:5 , DA D:6binding site for residue MG B 301
4AC4SOFTWAREGLU A:156 , DG C:4 , DC C:5 , DC C:6 , DC C:12 , DC D:5 , DA D:6 , DC D:12 , DA D:13binding site for residue MPD C 101
5AC5SOFTWAREGLU B:156 , DC C:5 , DC C:6 , DC C:12 , DG D:4 , DC D:5 , DA D:6 , DA D:13binding site for residue MPD C 102
6AC6SOFTWAREGLU A:73 , TRP A:77 , ARG B:72 , DA C:7 , DG C:8 , DG C:9 , DT C:10 , DG C:11 , DC D:7 , DT D:8 , DG D:10 , DG D:11binding site for residue MPD C 103
7AC7SOFTWARETRP B:77 , DG C:8 , DG C:9 , DC D:7 , DT D:8 , DT D:9binding site for residue MPD C 104

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:100 -Pro A:101
2Lys B:100 -Pro B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GKH)

(-) 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:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhhh.eeeeeeeeeeeee...eeeeeeeeeeeee.....eeee........eee....eeeeee...eeeeeee....eeeeeeeeeeeeeeee........eee.hhhhhhhhhhhhhhhh....eeeeeeee....eeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkh A   2 SKDKVTVITSPSTEELVSLVNSALLEEAMLTIFARCKVHYDGRAKSELGSGDRVIIVKPDGSFLIHQSKKREPVNWQPPGSRVRLELRENPVLVSIRRKPRETLEVELEEVYMVSVFRAEDYEELALTGSEAEMAELIFENPEVIEPGFKPLFREKAIGTGIVAVLGRDSDGNIVVLELKRRRAELHAVRQLKSYVEILREEYGDKVRGILVAPSLTSGAKRLLEKEGLEFRKLEPPKR 240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhhh.eeeeeeeeeeeee...eeeeeeeeeeeee.....eeee........eee....eeeeee...eeeeeee....eeeeeeeeeeeeeeee........eee.hhhhhhhhhhhhhhhh....eeeeeeee....eeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gkh B   2 SKDKVTVITSPSTEELVSLVNSALLEEAMLTIFARCKVHYDGRAKSELGSGDRVIIVKPDGSFLIHQSKKREPVNWQPPGSRVRLELRENPVLVSIRRKPRETLEVELEEVYMVSVFRAEDYEELALTGSEAEMAELIFENPEVIEPGFKPLFREKAIGTGIVAVLGRDSDGNIVVLELKRRRAELHAVRQLKSYVEILREEYGDKVRGILVAPSLTSGAKRLLEKEGLEFRKLEPPKR 240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         


Chain C from PDB  Type:DNA  Length:15
                                               
                 5gkh C   1 CGTGCCAGGTGCCGT  15
                                    10     


Chain D from PDB  Type:DNA  Length:15
                                               
                 5gkh D   1 ACGGCACTTGGCACG  15
                                    10
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5GKH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:100 - Pro A:101   [ RasMol ]  
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  5gkh
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  3.1.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        NUCS_THEKO | Q5JER9: 5gke 5gkf 5gkg 5gki 5gkj

(-) Related Entries Specified in the PDB File

5gke 5gkf 5gkg 5gki 5gkj