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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BDELLOVIBRIO BACTERIOVORUS NUCLEOSIDE DIPHOSPHATE SUGAR HYDROLASE
 
Authors :  S. B. Gabelli, A. H. De La Pena, A. Suarez, L. M. Amzel
Date :  24 Jun 15  (Deposition) - 20 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. H. De La Pena, A. Suarez, K. C. Duong-Ly, A. J. Schoeffield, M. A. Pizarro-Dupuy, M. Zarr, S. A. Pineiro, L. M. Amzel, S. B. Gabelli
Structural And Enzymatic Characterization Of A Nucleoside Diphosphate Sugar Hydrolase From Bdellovibrio Bacteriovorus
Plos One V. 10 41716 2015
PubMed-ID: 26524597  |  Reference-DOI: 10.1371/JOURNAL.PONE.0141716

(-) Compounds

Molecule 1 - NUDF PROTEIN
    ChainsA, B
    EC Number3.6.1.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System PlasmidPET24
    Expression System Taxid866768
    GeneNUDF, BD3179
    Organism ScientificBDELLOVIBRIO BACTERIOVORUS
    Organism Taxid264462
    StrainATCC 15356 / DSM 50701 / NCIB 9529 / HD100

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric/Biological Unit (5, 21)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PG02Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
4PGE2Ligand/IonTRIETHYLENE GLYCOL
5SO46Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:64 , LYS A:78 , GOL A:207 , HOH A:310 , HOH A:344 , HOH A:383binding site for residue SO4 A 201
02AC2SOFTWARETYR A:35 , THR A:36 , GLY A:179 , ARG B:18 , GLN B:138 , HOH B:302binding site for residue SO4 A 202
03AC3SOFTWAREARG A:64 , HOH A:303 , HOH A:367 , HOH A:402 , ARG B:37 , HOH B:356 , HOH B:364binding site for residue SO4 A 203
04AC4SOFTWARELEU A:51 , ARG A:127 , ASP A:128 , HOH A:305 , HOH A:316 , HOH A:366 , HOH A:401binding site for residue GOL A 204
05AC5SOFTWARETYR A:19 , LEU A:20 , LEU A:41 , PRO A:43 , LYS A:78 , HOH A:315 , HOH A:323 , HOH A:345binding site for residue GOL A 205
06AC6SOFTWARELYS A:69 , VAL A:70 , PHE A:71 , GLY A:159 , LYS A:160 , VAL A:161 , SER A:162 , HOH A:318 , HIS B:111binding site for residue GOL A 206
07AC7SOFTWAREHIS A:42 , ALA A:45 , GLU A:119 , LYS A:165 , SO4 A:201 , HOH A:351 , HOH A:377 , TYR B:116binding site for residue GOL A 207
08AC8SOFTWARELYS A:105 , PHE A:106 , LEU A:107 , TRP A:172 , TRP A:181 , HOH A:394binding site for residue PEG A 208
09AC9SOFTWAREGLN A:24 , GLN A:26 , THR A:36 , PHE A:176 , ASN A:182 , HOH A:308 , HOH A:311 , ARG B:18binding site for residue PEG A 209
10AD1SOFTWAREHIS A:61 , VAL A:70 , HOH A:376binding site for residue PG0 A 210
11AD2SOFTWAREPRO A:30 , GLY A:32 , GLU B:5 , GLN B:28 , ALA B:29binding site for residue PGE A 211
12AD3SOFTWAREARG A:37 , GLY A:115 , HOH A:312 , HOH A:339 , HOH A:341 , HOH A:343 , HOH A:356 , HOH A:420 , ARG B:64 , HOH B:346 , HOH B:358binding site for residue SO4 A 212
13AD4SOFTWAREARG A:18 , TYR A:19 , HOH A:333 , TYR B:35 , THR B:36 , HOH B:306 , HOH B:392 , HOH B:394binding site for residue SO4 A 213
14AD5SOFTWAREARG B:64 , GLY B:77 , LYS B:78 , GOL B:203 , HOH B:318 , HOH B:322 , HOH B:327 , HOH B:330 , HOH B:346 , HOH B:354binding site for residue SO4 B 201
15AD6SOFTWAREHIS A:111 , LYS B:69 , VAL B:70 , PHE B:71 , GLY B:159 , LYS B:160 , VAL B:161 , SER B:162 , PG0 B:207 , HOH B:334 , HOH B:409 , HOH B:421binding site for residue GOL B 202
16AD7SOFTWARETYR A:116 , HIS B:42 , GLU B:119 , LYS B:165 , SO4 B:201 , HOH B:327 , HOH B:357 , HOH B:388binding site for residue GOL B 203
17AD8SOFTWAREARG A:18 , HIS B:131 , HOH B:368 , HOH B:411binding site for residue GOL B 204
18AD9SOFTWAREHIS B:3 , LEU B:4 , GLU B:5binding site for residue GOL B 205
19AE1SOFTWARETYR A:116 , HOH A:365 , TYR B:19 , LEU B:20 , HIS B:42 , PRO B:43 , LYS B:78 , HOH B:335 , HOH B:336 , HOH B:382binding site for residue GOL B 206
20AE2SOFTWAREHIS B:61 , VAL B:70 , VAL B:145 , GOL B:202binding site for residue PG0 B 207
21AE3SOFTWARELYS B:105 , LEU B:107 , PHE B:176 , ASN B:182binding site for residue PGE B 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C7Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C7Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C7Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C7Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5C7Q)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeeee....eeeeeeee.....eeeeeee....eeeeee......eeeeeeee....eeeee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee..........eeeeeeeeeee...........eeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c7q A   1 MKHLEEKTLSTRQIFKGRYLKIEQDQVQAPDGRTYTREYILHPGAAMMIPLLPNGNVVMIHQYRHAVKKVFLEFPAGKRDHNEETLLTAKRELLEETGYEAKDWKFLTTIHPVIGYSNEHIDLYLARDLTHLEQRLDQGEFIEVVEVKPADLMQLVLEGKVSDVKTQIGAFWLDKFLRGEWN 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  

Chain B from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeee....eeeeeeee.....eeeeeee....eeeeeee.....eeeeeee......eeee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee..........eeeeeeeeeee...........eeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c7q B   3 HLEEKTLSTRQIFKGRYLKIEQDQVQAPDGRTYTREYILHPGAAMMIPLLPNGNVVMIHQYRHAVKKVFLEFPAGKRDHNEETLLTAKRELLEETGYEAKDWKFLTTIHPVIGYSNEHIDLYLARDLTHLEQRLDQGEFIEVVEVKPADLMQLVLEGKVSDVKTQIGAFWLDKFLRGEWN 182
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

   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 5C7Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C7Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C7Q)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q6MIH8_BDEBA | Q6MIH85c7t 5c8l

(-) Related Entries Specified in the PDB File

5c7t 5C7T CONTAINS THE SAME PROTEIN WITH ADPR