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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BINDING PROTEIN OPUAC IN COMPLEX WITH GLYCINE BETAINE
 
Authors :  C. Horn, L. Sohn-Boesser, J. Breed, W. Welte, L. Schmitt, E. Bremer
Date :  26 Sep 05  (Deposition) - 21 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Substrate-Binding Protein, Closed Liganded, Abc-Transporter, Compatible Solutes, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Horn, L. Sohn-Boesser, J. Breed, W. Welte, L. Schmitt, E. Bremer
Molecular Determinants For Substrate Specificity Of The Ligand-Binding Protein Opuac From Bacillus Subtilis For The Compatible Solutes Glycine Betaine And Proline Betaine.
J. Mol. Biol. V. 357 592 2006
PubMed-ID: 16445940  |  Reference-DOI: 10.1016/J.JMB.2005.12.085

(-) Compounds

Molecule 1 - GLYCINE BETAINE-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PBKB76
    Expression System Vector Type: PLASMID
    Gene: OPUAC
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1BET1Ligand/IonTRIMETHYL GLYCINE
2EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:21 , SER A:25 , GLY A:26 , ILE A:27 , TRP A:178 , GLU A:181 , TRP A:225 , THR A:229 , HIS A:230BINDING SITE FOR RESIDUE BET A 273
02AC2SOFTWAREILE A:19 , THR A:56BINDING SITE FOR RESIDUE EDO A 274
03AC3SOFTWAREARG A:63 , SER A:79 , ARG A:80 , ILE A:133 , HOH A:313BINDING SITE FOR RESIDUE EDO A 275
04AC4SOFTWARETYR A:93 , GLY A:94 , SER A:95 , ALA A:96 , VAL A:251 , MET A:253BINDING SITE FOR RESIDUE EDO A 276
05AC5SOFTWAREILE A:171 , ASN A:172 , THR A:200 , EDO A:278BINDING SITE FOR RESIDUE EDO A 277
06AC6SOFTWAREASN A:172 , GLY A:216 , SER A:217 , ALA A:218 , ASP A:219 , EDO A:277BINDING SITE FOR RESIDUE EDO A 278
07AC7SOFTWAREASP A:5 , GLU A:12 , HOH A:444BINDING SITE FOR RESIDUE EDO A 279
08AC8SOFTWARESER A:29 , ASP A:32 , LYS A:33BINDING SITE FOR RESIDUE EDO A 280
09AC9SOFTWARETHR A:54 , LYS A:58 , TRP A:76 , ARG A:80 , TYR A:81 , GLU A:136 , HOH A:329 , HOH A:440BINDING SITE FOR RESIDUE EDO A 281
10BC1SOFTWARELYS A:122 , TRP A:123 , SER A:247 , MET A:248 , THR A:249 , HOH A:336BINDING SITE FOR RESIDUE EDO A 282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B4L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:226 -Pro A:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B4L)

(-) Exons   (0, 0)

(no "Exon" information available for 2B4L)

(-) 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:268
 aligned with OPUAC_BACSU | P46922 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:268
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285        
          OPUAC_BACSU    26 DENASAAEQVNKTIIGIDPGSGIMSLTDKAMKDYDLNDWTLISASSAAMTATLKKSYDRKKPIIITGWTPHWMFSRYKLKYLDDPKQSYGSAEEIHTITRKGFSKEQPNAAKLLSQFKWTQDEMGEIMIKVEEGEKPAKVAAEYVNKHKDQIAEWTKGVQKVKGDKINLAYVAWDSEIASTNVIGKVLEDLGYEVTLTQVEAGPMWTAIATGSADASLSAWLPNTHKAYAAKYKGKYDDIGTSMTGVKMGLVVPQYMKNVNSIEDLKK 293
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eee.....hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhh.....eeeee..hhhhhh.eee...........eeeeeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhhhhhhhhhhh.eeeeee...hhhhhhhhh....eeeeeee...hhhhhhhh...eeeeeeeeeeeeeeeeee.......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4l A   5 DENASAAEQVNKTIIGIDPGSGIMSLTDKAMKDYDLNDWTLISASSAAMTATLKKSYDRKKPIIITGWTPHWMFSRYKLKYLDDPKQSYGSAEEIHTITRKGFSKEQPNAAKLLSQFKWTQDEMGEIMIKVEEGEKPAKVAAEYVNKHKDQIAEWTKGVQKVKGDKINLAYVAWDSEIASTNVIGKVLEDLGYEVTLTQVEAGPMWTAIATGSADASLSAWLPNTHKAYAAKYKGKYDDIGTSMTGVKMGLVVPQYMKNVNSIEDLKK 272
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
   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 2B4L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B4L)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OPUAC_BACSU | P46922)
molecular function
    GO:0050997    quaternary ammonium group binding    Interacting selectively and non-covalently with a quaternary ammonium group, including glycine betaine, choline, carnitine and proline. A quaternary ammonium group is any compound that can be regarded as derived from ammonium hydroxide or an ammonium salt by replacement of all four hydrogen atoms of the NH4+ ion by organic groups.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071705    nitrogen compound transport    The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    BET  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:226 - Pro A:227   [ 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 | Asym./Biol. Unit - sites 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
  2b4l
    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
  OPUAC_BACSU | P46922
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  OPUAC_BACSU | P46922
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        OPUAC_BACSU | P46922: 2b4m 3chg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2B4L)