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(-) Description

Title :  CRYSTAL STRUCTURE OF STEPTOCOCCUS PNEUMONIAE UNDECAPRENYL PYROPHOSPHATE SYNTHASE (UPPS) IN COMPLEX WITH ~{N}-(3-AZANYL-3-OXIDANYLIDENE-PROPYL)-5-(1-BENZOTHIOPHEN-5-YL)-1-(PHENYLMETHYL)-~{N}-[(4-PROPAN-2-YLOXYPHENYL)METHYL]PYRAZOLE-4-CARBOXAMIDE
 
Authors :  N. O. Concha
Date :  14 Jun 16  (Deposition) - 20 Jul 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Upps, Native, Bacterial, Undecaprenyl S. Pneumoniae, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Concha, J. Huang, X. Bai, A. Benowitz, P. Brady, L. C. Grady, L. H. Kryn, D. Holmes, K. Ingraham, Q. Jin, L. Pothier Kaushansky, L. Mccloskey, J. A. Messer, H. O'Keefe, A. Patel, A. L. Satz, R. H. Sinnamon, J. Schneck, S. R. Skinner, J. Summerfield, A. Taylor, J. D. Taylor, G. Evindar, R. A. Stavenger
Discovery And Characterization Of A Class Of Pyrazole Inhibitors Of Bacterial Undecaprenyl Pyrophosphate Synthase
J. Med. Chem. V. 59 7299 2016
PubMed-ID: 27379833  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00746

(-) Compounds

Molecule 1 - ISOPRENYL TRANSFERASE
    Chains: A, B
    EC Number: 2.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UPPS, SP_0261
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE SEROTYPE 4 (STRAIN ATCC BAA-334 / TIGR4)
    Organism Taxid: 170187
    Strain: ATCC BAA-334 / TIGR4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
16TC1Ligand/Ion~{N}-(3-AZANYL-3-OXIDANYLIDENE-PROPYL)-5-(1-BENZOTHIOPHEN-5-YL)-1-(PHENYLMETHYL)-~{N}-[(4-PROPAN-2-YLOXYPHENYL)METHYL]PYRAZOLE-4-CARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET B:27 , ASN B:30 , HIS B:45 , ALA B:71 , ILE B:87 , LEU B:90 , PRO B:91 , PHE B:94 , LEU B:118 , LEU B:126 , PHE B:143 , TRP B:227binding site for residue 6TC B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KH5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KH5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KH5)

(-) Exons   (0, 0)

(no "Exon" information available for 5KH5)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeee..................eeee...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kh5 A  17 TQVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFSTENRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNRRHRR 248
                                    26        36        46        56        66        76|       88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
                                                                                      76|                                                                                                                                                                         
                                                                                       79                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...eeee..................eeee...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kh5 B  17 TQVPAHIGIIMDGNGRWAKKRMQPRVFGHKAGMEALQTVTKAANKLGVKVITVYAFTRPDQEVKFIMNLPVEFYDNYVPELHANNVKIQMIGETDRLPKQTFEALTKAEELTKNNTGLILNFALNYGGRAEITQALKLISQDVLDAKINPGDITEELIGNYLFTQHLPKDLRDPDLIIRTSGELRLSNFLPWQGAYSELYFTDTLWPDFDEAALQEAILAYNRRH 246
                                    26        36        46        56        66     || 81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
                                                                                  72|                                                                                                                                                                        
                                                                                   78
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  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 5KH5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KH5)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        ISPT_STRPN | Q97SR4: 5kh2 5kh4

(-) Related Entries Specified in the PDB File

5kh2 5kh4