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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI BETA CLAMP BOUND TO DNA LIGASE PEPTIDE
 
Authors :  P. Pandey, S. Gourinath
Date :  21 Dec 15  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,G,L
Biol. Unit 1:  A,D,G  (1x)
Biol. Unit 2:  B,C,L  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Pandey, K. F. Tarique, M. Mazumder, S. A. Abdul Rehman, S. Gourinat
Structural Insight Into Beta-Clamp And Its Interaction With Dna Ligase In Helicobacter Pylori
Sci. Rep. V. 6 31181 2016
PubMed-ID: 27499105  |  Reference-DOI: 10.1038/SREP31181

(-) Compounds

Molecule 1 - DNA POLYMERASE III SUBUNIT BETA
    Chains: A, C, B, D
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28(B)
    Expression System Vector Type: PLASMID
    Organ: STOMACH LINING, UPPER INTESTINAL LINING
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695
    Synonym: BETA CLAMP
 
Molecule 2 - DNA LIGASE
    Chains: G, L
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDGL
Biological Unit 1 (1x): A  DG 
Biological Unit 2 (1x):  BC  L

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FRQ)

(-) Sites  (0, 0)

(no "Site" information available for 5FRQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FRQ)

(-) Sequences/Alignments

Asymmetric 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhh......hhh.eeeeeee..eeeeeee...eeeeeeee..eeee.eeeeeehhhhhhhhhh....eeeeeee..eeeeee..eeeeee..hhhhh.........eeeee..hhhhhhhhhhhhhh.....hhhh.eeeeeee.hhheeeeeee...eeeeeee.....ee...eeeeeeehhhhhhhhhhh...eeeee...eeeee....eeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh...eeeeee...eeeeee...eeeeeee.........eeeeeehhhhhhhhhh....eeeeee......eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5frq A   1 MKISVSKNDLENALRYLQAFLDKKDASSIASHIHLEVIKEKLFLKASDSDIGLKSYIFTQSSDKEGVGTINGKKFLDIISCLKDSNIILETKDDSLAIKQNKSSFKLPMFDADEFPEFPVIDPKVSIEVNAPFLVDAFKKIAPVIEQTSHKRELAGILMQFDQKHQTLSVVGTDTKRLSYTQLEKISIHSTEEDISCILPKRALLEILKLFYENFSFKSDGMLAVIENEMHTFFTKLIDGNYPDYQKILPKEYISSFTLGKEEFKESIKLCSSLSSTIKLTLEKNNALFESLSETAKTSVEIEKGLDIEAFHLGVNAKFFLEALNALGTTQFVLRCNEPSSPFLIQESKISTLMMPIT 373
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 ||    304       315       325       335       345       365        
                                                                                                                                                                                                                                                                                                                             292|             313|                                   353|         
                                                                                                                                                                                                                                                                                                                              297              315                                    364         


Chain B from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhh......hhh.eeeeeee..eeeeeee...eeeeeeee..eeee..eeeeehhhhhhhhhhh...eeeeeee..eeeeee..eeeeee..hhhhh.........eeeee..hhhhhhhhhhhhhh.....hhhh.eeeeeee....eeeeeee...eeeeeee.....ee...eeeeeeehhhhhhhhhhh...eeeee...eeeee....eeeee.......hhhhh.......eeeeehhhhhhhhhhhhh...eeeeee...eeeeee.......eeeeeee.........eeeeeehhhhhhhhhh....eeeee.......eeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5frq B   1 MKISVSKNDLENALRYLQAFLDKKDASSIASHIHLEVIKEKLFLKASDSDIGLKSYIFTQSSDKEGVGTINGKKFLDIISCLKDSNIILETKDDSLAIKQNKSSFKLPMFDADEFPEFPVIDPKVSIEVNAPFLVDAFKKIAPVIEQTSHKRELAGILMQFDQKHQTLSVVGTDTKRLSYTQLEKISIHSTEEDISCILPKRALLEILKLFYENFSFKSDGMLAVIENEMHTFFTKLIDGNYPDYQKILPKEYISSFTLGKEEFKESIKLCSSLSSTIKLTLEKNNALFESLDSEHSETAKTSVEIEKGLDIEAFHLGVNAKFFLEALNALGTTQFVLRCNEPSSPFLIQESLKISTLMMPITL 374
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  ||   321       331       341       351  ||   370    
                                                                                                                                                                                                                                                                                                                                                  313|                                    354|          
                                                                                                                                                                                                                                                                                                                                                   315                                     364          


Chain C from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhh......hhh.eeeeeee..eeeeeee...eeeeeeee..eeee.eeeeeehhhhhhhhhhh...eeeeeee..eeeeee..eeeeee..hhhhh.........eeeee..hhhhhhhhhhhhhh.....hhhh.eeeeeee....eeeeeee...eeeeeee.....ee....eeeeeehhhhhhhhhhh...eeeee...eeeee....eeeee.......hhhhh......eeeeeehhhhhhhhhhhhh...eeeeee...eeeeee..eeeeeee..........eeeeeehhhhhhhhhh....eeeeee......eeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5frq C   1 MKISVSKNDLENALRYLQAFLDKKDASSIASHIHLEVIKEKLFLKASDSDIGLKSYIFTQSSDKEGVGTINGKKFLDIISCLKDSNIILETKDDSLAIKQNKSSFKLPMFDADEFPEFPVIDPKVSIEVNAPFLVDAFKKIAPVIEQTSHKRELAGILMQFDQKHQTLSVVGTDTKRLSYTQLEKISIHSTEEDISCILPKRALLEILKLFYENFSFKSDGMLAVIENEMHTFFTKLIDGNYPDYQKILPKEYISSFTLGKEEFKESIKLCSSLSSTIKLTLEKNNALFESLETAKTSVEIEKGLDIEKAFHLGVNAKFFLEALNALGTTQFVLRCNEPSSPFLIQESKISTLMMPIT 373
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 ||    305       315       325       335       345       365        
                                                                                                                                                                                                                                                                                                                             292|                                                    353|         
                                                                                                                                                                                                                                                                                                                              298                                                     364         


Chain D from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhh....hhh.eeeeeee..eeeeeee...eeeeeeee..eeee.eeeeeehhhhhhhhhh.....eeeeee..eeeeee..eeeeee................eeeee..hhhhhhhhhhhhhh.....hhhh.eeeeeee.hhheeeeeee...eeeeeee.....ee...eeeeeeehhhhhhhhhhh...eeeee...eeeee....eeeee.......hhhhhh.....eeeeeehhhhhhhhhhhhh...eeeeee...eeeee...eeeeeee..........eeeeeehhhhhhhhhh....eeeeee......eeeee...eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5frq D   1 MKISVSKNDLENALRYLQAFLDDASSIASHIHLEVIKEKLFLKASDSDIGLKSYIFTQSSDKEGVGTINGKKFLDIISCLKDSNIILETKDDSLAIKQNKSSFKLPMFDADEFPEFPVIDPKVSIEVNAPFLVDAFKKIAPVIEQTSHKRELAGILMQFDQKHQTLSVVGTDTKRLSYTQLEKISIHSTEEDISCILPKRALLEILKLFYENFSFKSDGMLAVIENEMHTFFTKLIDGNYPDYQKILPKEYISSFTLGKEEFKESIKLCSSLSSTIKLTLEKNNALFESSETAKTSVEIEKGLDIEKAFHLGVNAKFFLEALNALGTTQFVLRCNEPSSPFLIQESKISTLMMPITL 374
                                    10        20 ||     32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       297       307       317       327       337       347     ||367       
                                                22|                                                                                                                                                                                                                                                                       291|                                                     353|          
                                                 25                                                                                                                                                                                                                                                                        297                                                      364          


Chain G from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5frq G 370 FIRSLF 375


Chain L from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5frq L 370 FIRSLF 375
   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 5FRQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 20)

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        DPO3B_HELPY | O25242: 4rki 4s3i 5fve 5g48 5g4q

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