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 :  PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH ACETAMIDE BOUND
 
Authors :  J. N. Henderson, E. G. Sweeney, J. Goers, C. Wreden, K. G. Hicks, R. Parth K. J. Guillemin, S. J. Remington
Date :  23 Oct 11  (Deposition) - 27 Jun 12  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Four-Helix Bundle, Pas Domain, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Goers Sweeney, J. N. Henderson, J. Goers, C. Wreden, K. G. Hicks, J. K. Foster, R. Parthasarathy, S. J. Remington, K. Guillemin
Structure And Proposed Mechanism For The Ph-Sensing Helicobacter Pylori Chemoreceptor Tlpb.
Structure V. 20 1177 2012
PubMed-ID: 22705207  |  Reference-DOI: 10.1016/J.STR.2012.04.021

(-) Compounds

Molecule 1 - CHEMORECEPTOR TLPB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBH4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PERIPLASMIC PORTION
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 102617
    Strain: SS1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACM2Ligand/IonACETAMIDE
2GOL2Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:103 , ASP A:114 , VAL A:116 , TYR A:136 , TYR A:140 , TYR A:153 , LYS A:166 , HOH A:407BINDING SITE FOR RESIDUE ACM A 301
2AC2SOFTWARELYS A:54 , ARG A:55 , THR A:58 , MET A:99 , HOH A:511 , HOH A:619 , LYS B:54 , SO4 B:303 , HOH B:510 , HOH B:512BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREVAL B:103 , ASP B:114 , VAL B:116 , TYR B:136 , TYR B:140 , TYR B:153 , LYS B:166 , HOH B:407BINDING SITE FOR RESIDUE ACM B 301
4AC4SOFTWAREASN B:94 , ASP B:95 , LYS B:157 , TYR B:158 , HOH B:408 , HOH B:411 , HOH B:415 , HOH B:448 , HOH B:456 , HOH B:507 , HOH B:616BINDING SITE FOR RESIDUE GOL B 302
5AC5SOFTWARELYS A:54 , SO4 A:302 , LYS B:54 , ARG B:55 , THR B:58 , MET B:99 , HOH B:510 , HOH B:511 , HOH B:512 , HOH B:537BINDING SITE FOR RESIDUE SO4 B 303
6AC6SOFTWARELYS B:97 , GLY B:98 , MET B:99 , ASP B:188 , GLU B:192 , HOH B:420 , HOH B:494 , HOH B:498BINDING SITE FOR RESIDUE GOL B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UB7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UB7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UB7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UB7)

(-) Exons   (0, 0)

(no "Exon" information available for 3UB7)

(-) 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:160
 aligned with B6JPK4_HELP2 | B6JPK4 from UniProtKB/TrEMBL  Length:561

    Alignment length:160
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198
         B6JPK4_HELP2    39 QLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKNFDNATARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENQAIKEGVN 198
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....eee...hhhhh.............hhhhhhhhhhhh..eeeeeee........eeeeeeeeee....eeeeeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ub7 A  42 QLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKSFDNDTARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENKAIKEGVN 201
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with B6JPK4_HELP2 | B6JPK4 from UniProtKB/TrEMBL  Length:561

    Alignment length:161
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197 
         B6JPK4_HELP2    38 AQLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKNFDNATARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENQAIKEGVN 198
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee....eee...hhhhh.............hhhhhhhhhhhh..eeeeeee........eeeeeeeeee....eeeeeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ub7 B  41 AQLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKSFDNDTARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENKAIKEGVN 201
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 3UB7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UB7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UB7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B6JPK4_HELP2 | B6JPK4)
molecular function
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    ACM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ub7)
 

(-) 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
  3ub7
    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
  B6JPK4_HELP2 | B6JPK4
    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
  B6JPK4_HELP2 | B6JPK4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B6JPK4_HELP2 | B6JPK4: 3ub6 3ub8 3ub9

(-) Related Entries Specified in the PDB File

3ub6 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH UREA BOUND
3ub8 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH FORMAMIDE BOUND
3ub9 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH HYDROXYUREA BOUND