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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF STREPTOCOCCUS MUTANS COMA
 
Authors :  S. Ishii, K. Fukui, S. Yokoshima, K. Kumagai, Y. Beniyama, T. Kodama, T. T. Okabe, T. Nagano, H. Kojima, T. Yano
Date :  03 Apr 17  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Peptidase, Quorum-Sensing, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ishii, K. Fukui, S. Yokoshima, K. Kumagai, Y. Beniyama, T. Kodama, T. Fukuyama, T. Okabe, T. Nagano, H. Kojima, T. Yano
High-Throughput Screening Of Small Molecule Inhibitors Of The Streptococcus Quorum-Sensing Signal Pathway
Nat Commun 2017
PubMed: search  |  Reference-DOI: 10.1038/S41598-017-03567-2

(-) Compounds

Molecule 1 - PUTATIVE ABC TRANSPORTER, ATP-BINDING PROTEIN COMA
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21B
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SMU_286
    Organism Scientific: STREPTOCOCCUS MUTANS SEROTYPE C
    Organism Taxid: 210007
    Other Details: THE FIRST METHIONINE AND THE LAST 16 RESIDUES ARE NOT IDENTIFIED IN THE CRYSTAL STRUCTURE.
    Strain: ATCC 700610 / UA159

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA C:23 , SER C:24binding site for residue PEG C 201
2AC2SOFTWARELEU C:38 , ARG C:39binding site for residue PEG C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5XE8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:82 -Pro A:83
2Tyr C:82 -Pro C:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XE8)

(-) Exons   (0, 0)

(no "Exon" information available for 5XE8)

(-) 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:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh......hhhhhhhhh.......hhhhhhhhhhhh..eeeeee.hhhhhhh......eeeeeee..eeeeeeeeeeee..eeeeee.....eeeeeehhhhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xe8 A   6 YKLVPQIDTRDCGPAVLASVAKHYGSNYSIAYLRELSKTNKQGTTALGIVEAAKKLGFETRSIKADMTLFDYNDLTYPFIVHVIKGKRLQHYYVVYGSQNNQLIIGDPDPSVKVTRMSKERFQSEWTGLAIFLAP 140
                                    15        25        35        45        55        65        75        85        95       105       115       125       135     


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhh.hhhhh......hhhhhhhhhhhh..eeeeee.hhhhhhh......eeeeeee..eeeeeeeeeeee..eeeeee.....eeeeeehhhhhhheeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xe8 C   6 YKLVPQIDTRDCGPAVLASLRELSKTNKQGTTALGIVEAAKKLGFETRSIKADMTLFDYNDLTYPFIVHVIKGKRLQHYYVVYGSQNNQLIIGDPDPSVKVTRMSKERFQSEWTGLAIFLAP 140
                                    15        38        48        58        68        78        88        98       108       118       128       138  
                                             24|                                                                                                      
                                              38
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  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 5XE8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5XE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XE8)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  5xe8
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q8DW05_STRMU | Q8DW05: 5xe9
UniProtKB/TrEMBL
        Q8DW05_STRMU | Q8DW05: 3k8u 3vx4

(-) Related Entries Specified in the PDB File

5xe9