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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE FROM ACINETOBACTER BAUMANNII, SPACE GROUP P212121
 
Authors :  K. H. Huynh, M. K. Hong, L. W. Kang
Date :  09 Sep 15  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  D-Alanine-D-Alanine Ligase, Acinetobacter Baumannii, Drug Target Protein, Apo Structure, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Huynh, M. K. Hong, C. Lee, H. T. Tran, S. H. Lee, Y. J. Ahn, S. S. Cha, L. W. Kang
The Crystal Structure Of The D-Alanine-D-Alanine Ligase Fro Acinetobacter Baumannii Suggests A Flexible Conformational Change In The Central Domain Before Nucleotide Binding
J. Microbiol. V. 53 776 2015
PubMed-ID: 26502962  |  Reference-DOI: 10.1007/S12275-015-5475-8

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B, C, D, E, F
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DDL, ACICU_03532
    Organism Scientific: ACINETOBACTER BAUMANNII ACICU
    Organism Taxid: 405416
    Strain: ACICU
    Synonym: D-ALA-D-ALA LIGASE,D-ALANYLALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5DMX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ile A:223 -Pro A:224
2Leu B:135 -Pro B:136
3Ile B:223 -Pro B:224
4Leu C:135 -Pro C:136
5Ile C:223 -Pro C:224
6Leu D:135 -Pro D:136
7Ile D:223 -Pro D:224
8Ile E:223 -Pro E:224
9Leu F:135 -Pro F:136
10Ile F:223 -Pro F:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DMX)

(-) 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:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhheeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......ee.....ee....eeeeeeeee..ee...ee.........hhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dmx A   1 MSNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIIVVMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLE 305
                                    10        20        30        40        50        60        70        80        90       100       110       120|      181       191       221       231       241       251       261       271       281       291       301    
                                                                                                                                                 120|                         200|                                                                                    
                                                                                                                                                  172                          221                                                                                    


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh..eeeee......eeeee...eeeeeeeee..ee...ee.........hhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmx B   2 SNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITKETDLDSVIAELGLPVIIKPVHEGAVVMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLE 305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   ||  176       186       196   ||  226       236       246       256       266       276       286       296         
                                                                                                                                                                         145|                          200|                                                                                    
                                                                                                                                                                          171                           221                                                                                    


Chain C from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......ee....hhhhhhhh..eee.......eee...eeeeeeeee..ee...ee.........hhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmx C   1 MSNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITLDSVIAELGLPVIIKPVHEGMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLE 305
                                    10        20        30        40        50        60        70        80        90       100       110       120||     134       144||     182       192       222       232       242       252       262       272       282       292       302   
                                                                                                                                                  121|                145|                       200|                                                                                    
                                                                                                                                                   126                 174                        221                                                                                    


Chain D from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.......eee.....hhhhhhhhhh..eeeee.............hhhhhh.........eeeee...eeeeeeeee..ee...ee.........hhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dmx D   4 ATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITKETDLDSVIAELGLPVIIKPVHEVGMSKVEKAEDFAAAIEKATQHDAVVMAEKWITGREFTISFLNGQPLPVIRLGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTL 304
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143||     156       166       176       186       196  ||   228       238       248       258       268       278       288       298      
                                                                                                                                                                      144|                                                199|                                                                                  
                                                                                                                                                                       148                                                 222                                                                                  


Chain E from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh............ee..ee................hhhhhhhhhhhhh.................hhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmx E   4 ATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYFTISFLNGQPLPVIRLQYGIPCLSEKKLQALCLRAFQAVGAEGRIEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLE 305
                                    13        23        33        43        53        63        73        83        93       103       113   ||  189       199||   ||233       243     ||268       278       288       298       
                                                                                                                                           117|             200| 225| ||             249| ||                                     
                                                                                                                                            184              221  227 ||              252 ||                                     
                                                                                                                                                                    229|                254|                                     
                                                                                                                                                                     233                 268                                     


Chain F from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhheeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...........hhhhhhhh........eeeeeeeee..ee...ee.........hhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmx F   1 MSNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRILDSVIAELGLPAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLE 305
                                    10        20        30        40        50        60        70        80        90       100       110       126       136|      184       194     ||224       234       244       254       264       274       284       294       304 
                                                                                                                                                119|       136|                      200|                                                                                    
                                                                                                                                                 126        175                       221
   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 5DMX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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  Cis Peptide Bonds
    Ile A:223 - Pro A:224   [ RasMol ]  
    Ile B:223 - Pro B:224   [ RasMol ]  
    Ile C:223 - Pro C:224   [ RasMol ]  
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        DDL_ACIBC | B2I1J3: 5d8d

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