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(-) Description

Title :  CRYSTAL STRUCTURE OF CSD1-CSD2 DIMER I
 
Authors :  D. R. An, S. W. Suh
Date :  29 Mar 16  (Deposition) - 19 Oct 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  M23B Family Metallopeptidase, Heterodimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. An, H. N. Im, J. Y. Jang, H. S. Kim, J. Kim, H. J. Yoon, D. Hesek, M. Lee S. Mobashery, S. J. Kim, S. W. Suh
Structural Basis Of The Heterodimer Formation Between Cell Shape-Determining Proteins Csd1 And Csd2 From Helicobacter Pylori
Plos One V. 11 64243 2016
PubMed-ID: 27711177  |  Reference-DOI: 10.1371/JOURNAL.PONE.0164243

(-) Compounds

Molecule 1 - TOXR-ACTIVATED GENE (TAGE)
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 125-312
    Gene: HP_1543
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: ATCC 700392 / 26695
 
Molecule 2 - TOXR-ACTIVATED GENE (TAGE)
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 121-308
    Gene: HP_1544
    Organism Scientific: HELICOBACTER PYLORI (STRAIN ATCC 700392 / 26695)
    Organism Taxid: 85962
    Strain: ATCC 700392 / 26695

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:168 , ASP A:173 , HIS A:219 , HIS A:250 , HIS A:252binding site for residue ZN A 401
2AC2SOFTWAREASP B:303 , HOH B:401 , HIS C:169 , ASP C:173 , HIS C:252 , HOH C:514binding site for residue ZN C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J1L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:169 -Thr A:170
2Val B:300 -Asp B:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J1L)

(-) Exons   (0, 0)

(no "Exon" information available for 5J1L)

(-) 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:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.....hhhhhhhhh.ee....eeee.....eee....eeeeeee..hhhhh.eeeeee....eeeeeeee.ee......ee....eeee..........eeeeeeee..eee.hhhhhh......hhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j1l A 129 GLQKSFIMRLIPNDYPLESYRRVSAVLHNHTGLDLSTAINTPVYASASGVVGLASKGWNGGYGNLIKVFHPFGFKTYYAHLNKIVVKTGEFVKKGQLIGYSGNTGMSTGPHLHYEVRFLDQPINPMSFTKWNMKDFEEVFNKERSIRWQSLITIINRLMQ 299
                                   138       148    || 169       179       189       199       209       219       229       239       249       259       269       279       289       299
                                                  153|                                                                                                                                      
                                                   165                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..........eeee.hhh.............eeee.....eee....eeeeeee........eeeeee....eeeeeeeeeee......ee....eeeee.........eeeeeeee..ee.hhhhhhh.......hhhhh....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j1l B 123 NLNLAQKHLALMLIPNGMPIKTYSAIKPTKERNHPIKKIKGVESGIDFIAPLNTPVYASADGIVDFVKTNSNVGYGNLVRIEHAFGFSSIYTHLDHVNVQPKSFIQKGQLIGYSGKSGNSGGEKLHYEVRFLGKILDAQKFLAWDLDHFQSALEENKFIEWKNLFWVLEDIVQLQEHVDKDA 304
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302  


Chain C from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..........eeee.......eeee.....eee....eeeeeee..hhhhh.eeeeee....eeeeeeee.ee......ee....eeee..........eeeeeeee..eee.hhhhhh......hhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j1l C 127 ITGLQKSFIMRLIPNDYPLESYRRVSAAFNNHTGLDLSTAINTPVYASASGVVGLASKGWNGGYGNLIKVFHPFGFKTYYAHLNKIVVKTGEFVKKGQLIGYSGNTGMSTGPHLHYEVRFLDQPINPMSFTKWNMKDFEEVFNKERSIRWQSLITIINRLMQ 299
                                   136       146       156|      177       187       197       207       217       227       237       247       257       267       277       287       297  
                                                       156|                                                                                                                                   
                                                        168                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..........eeee.hhh.............eeee.....eee....eeeeeee........eeeeee....eeeeeeee.ee......ee....eeee..........eeeeeeee..ee.hhhhhhh.....hhhhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j1l D 123 NLNLAQKHLALMLIPNGMPIKTYSAIKPTKERNHPIKKIKGVESGIDFIAPLNTPVYASADGIVDFVKTNSNVGYGNLVRIEHAFGFSSIYTHLDHVNVQPKSFIQKGQLIGYSGKSGNSGGEKLHYEVRFLGKILDAQKFLAWDLDHFQSALEENKFIEWKNLFWVLEDIVQLQ 297
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
   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 5J1L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J1L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J1L)

(-) Gene Ontology  (2, 4)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5j1k 5j1m