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(-) Description

Title :  CRYSTAL STRUCTURE OF LUXP IN COMPLEX WITH A FORMOSE DERIVED AI-2 ANALOGUE
 
Authors :  M. A. Mcdonough, S. Sattin, P. M. Gardner, C. Liu, B. G. Davis
Date :  12 Mar 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Ligand Complex, Quorum Sensing, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Sattin
Discovery Of Glycomimetic Agonists From A Protocell Metabolism, Proto-Natural Product Libraries
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AUTOINDUCER 2-BINDING PERIPLASMIC PROTEIN LUXP
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX4T1
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 24-365
    GeneLUXP
    Organism ScientificVIBRIO HARVEYI
    Organism Taxid669

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
14EX2Ligand/Ion1-DEOXY-2,3-O-(DIHYDROXYMETHYLIDENE)-BETA-L-XYLULOFURANOSE
2CA1Ligand/IonCALCIUM ION
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:217 , ASP A:283 , HOH A:502 , HOH A:503 , HOH A:504 , HOH A:505binding site for residue MG A 401
2AC2SOFTWAREHOH A:542 , HOH A:544 , HOH A:547 , HOH A:572binding site for residue MG A 402
3AC3SOFTWAREGLN A:77 , SER A:79 , TYR A:81 , TRP A:82 , ASN A:159 , PHE A:206 , ARG A:215 , SER A:265 , THR A:266 , TRP A:289 , ARG A:310 , HOH A:549binding site for residue 4EX A 403
4AC4SOFTWAREASP B:217 , ASP B:283 , HOH B:503 , HOH B:511 , HOH B:518binding site for residue CA B 401
5AC5SOFTWARESER B:79 , TYR B:81 , TRP B:82 , ASN B:159 , ARG B:215 , SER B:265 , THR B:266 , TRP B:289 , ARG B:310 , HOH B:554binding site for residue 4EX B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YP9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala B:111 -Asp B:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YP9)

(-) Exons   (0, 0)

(no "Exon" information available for 4YP9)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeeee.................eeeee..hhhhhhhhhhhhhh...eeeee.....hhhhh.....eeee.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh....ee.....hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh......eee..eeeee...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yp9 A  23 MVLNGYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNASLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQPFLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSD 364
                                    32        42        52        62        72        82        92       102       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       
                                                                                                                  111|                                                                                                                                                                                                                                                       
                                                                                                                   117                                                                                                                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhh..eeeee.....hhhhh.....eeee.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh....ee.....hhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhh......eee..eeeee...hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yp9 B  23 MVLNGYWGYQEFLDEFPEQRNLTNALSEAVRAQPVPLSKPTQRPIKISVVYPGQQVSDYWVRNIASFEKRLYKLNINYQLNQVFTRPNADIKQQSLSLMEALKSKSDYLIFTLDTTRHRKFVEHVLDSTNTKLILQNITTPVREWDKHQPFLYVGFDHAEGSRELATEFGKFFPKHTYYSVLYFSEGYISDVRGDTFIHQVNRDNNFELQSAYYTKATKQSGYDAAKASLAKHPDVDFIYACSTDVALGAVDALAELGREDIMINGWGGGSAELDAIQKGDLDITVMRMNDDTGIAMAEAIKWDLEDKPVPTVYSGDFEIVTKADSPERIEALKKRAFRYSD 364
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362  

   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 4YP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YP9)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:111 - Asp B:112   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        LUXP_VIBHA | P543001jx6 1zhh 2hj9 4yr7 4yrz

(-) Related Entries Specified in the PDB File

1jx6