Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  LACTOCOCCAL OPPA COMPLEXED WITH SLSQLSSQS
 
Authors :  R. P. -A. Berntsson, A. -M. W. H. Thunnissen, B. Poolman, D. -J. Slotboom
Date :  11 May 11  (Deposition) - 29 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Substrate-Binding Protein, Peptide Binding, Membrane Anchored, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Berntsson, A. M. Thunnissen, B. Poolman, D. J. Slotboom
Importance Of A Hydrophobic Pocket For Peptide Binding In Lactococcal Oppa.
J. Bacteriol. V. 193 4254 2011
PubMed-ID: 21665971  |  Reference-DOI: 10.1128/JB.00447-11

(-) Compounds

Molecule 1 - OLIGOPEPTIDE-BINDING PROTEIN OPPA
    Chains: A
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Strain: MG1363
    Expression System Taxid: 416870
    Gene: OPPA, LLMG_0701
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 416870
    Strain: MG1363
 
Molecule 2 - OLIGOPEPTIDE
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3RYA)

(-) Sites  (0, 0)

(no "Site" information available for 3RYA)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RYA)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:257 -Val A:258
2Pro A:460 -Pro A:461

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RYA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RYA)

(-) Exons   (0, 0)

(no "Exon" information available for 3RYA)

(-) 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:559
 aligned with A2RJ53_LACLM | A2RJ53 from UniProtKB/TrEMBL  Length:600

    Alignment length:559
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588         
         A2RJ53_LACLM    39 GNFDVAYQNPDKAIKGGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGSDRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSITYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSVKGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNFGHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGVSSAKL 597
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------SBP_bac_5-3ryaA01 A:80-495                                                                                                                                                                                                                                                                                                                                                                                                      -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeee..........hhhhh.hhhhhhhh..hhhhhh...............eeeeee....eeeeee............hhhhhhhhhhhhhhhhhh......hhhhh.hhhhhhh........ee........eeeee....hhhhhh...........hhhhhh..hhhhhhhhhhhh........eeeeeee...eeeeee..........eeeeeee.....hhhhhhhh....eee..hhhhhhhhhh...eeee.....eeeeeee...eee....eee....hhhhhhhhhhhhhhhhhhhhhhhhhh...eee........hhhhh..........hhhhhhhhhhh...ee......eee..ee.eeeee......hhhhhhhhhhhhhhhh..eeee.hhh..hhhhhhhhhhh........eeeeeee......hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.eee...eeee.............hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rya A  17 GNFDVAYQNPDKAIKGGNLKVAYQSDSPMKAQWLSGLSNDATFATMSGPGGGQDGLFFTDSGFKFIKGGAADVALDKESKTATITLRKDLKWSDGSEVTAKDYEFTYETIANPAYGSDRWTDSLANIVGLSDYHTGKAKTISGITFPDGENGKVIKVQFKEMKPGMTQSGNGYFLETVAPYQYLKDVAPKDLASSPKTTTKPLVTGPFKPENVVAGESIKYVPNPYYWGEKPKLNSITYEVVSTAKSVAALSSSKYDIINGMVSSQYKQVKNLKGYKVLGQQAMYISLMYYNLGHYDAKNSINVQDRKTPLQDQNVRQAIGYARNVAEVDNKFSNGLSTPANSLIPPIFKQFTSSSVKGYEKQDLDKANKLLDEDGWKLNKSTGYREKDGKELSLVYAARVGDANAETIAQNYIQQWKKIGVKVSLYNGKLMEFNSWVDHMTTPPGANDWDITDGSWSLASEPSQQDLFSAAAPYNFGHFNDSEITKDLNDIDSAKSENPTYRKAAFVKYQEDMNKKAYVIPTNFMLNYTPVNKRVVGMTLDYGAMNTWSEIGVSSAKL 575
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566         


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ...eee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3rya B   1 SLSQLSSQS   9
   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 3RYA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RYA)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A2RJ53_LACLM | A2RJ53)
biological process
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0043190    ATP-binding cassette (ABC) transporter complex    A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3rya)
 
  Sites
(no "Sites" information available for 3rya)
 
  Cis Peptide Bonds
    Pro A:460 - Pro A:461   [ RasMol ]  
    Val A:257 - Val A:258   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3rya
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A2RJ53_LACLM | A2RJ53
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A2RJ53_LACLM | A2RJ53
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A2RJ53_LACLM | A2RJ53: 3drf 3drg 3drh 3dri 3drj 3drk 3fto 3ryb

(-) Related Entries Specified in the PDB File

3drf 3drg 3drh 3dri 3drj 3drk 3fto 3ryb