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 :  CRYSTAL STRUCTURE OF RECOMBINANT TP0435 FROM TREPONEMA PALLIDUM
 
Authors :  C. A. Brautigam, R. K. Deka, M. V. Norgard
Date :  22 Jul 14  (Deposition) - 22 Oct 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lipoprotein, Disulfide-Linked Dimer, Beta Barrel, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Brautigam, R. K. Deka, W. Z. Liu, M. V. Norgard
Insights Into The Potential Function And Membrane Organization Of The Tp0435 (Tp17) Lipoprotein From Treponem Pallidum Derived From Structural And Biophysical Analyses.
Protein Sci. V. 24 11 2015
PubMed-ID: 25287511  |  Reference-DOI: 10.1002/PRO.2576
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 17 KDA LIPOPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PE-SUMOPRO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SOLUBLE DOMAIN (UNP RESIDUES 33-154)
    Gene: TPP17, TP_0435
    Organism Scientific: TREPONEMA PALLIDUM
    Organism Taxid: 243276
    Strain: NICHOLS

 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 4U3Q)

(-) Sites  (0, 0)

(no "Site" information available for 4U3Q)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:18 -B:18

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U3Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4U3Q)

(-) 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:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.eeeeee...eeeeee....eeeeeee..eeeeeeeee.....eeeeee.eeeeeeee..eeeeee.....hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4u3q A  10 KAKAEKVECALKGGIFRGTLPIDTTVTFNADGTAQKVELSPLTYRGTWMVREDGIVELSLVEKELYELIDSNSVRYMGAPGAEMAPFYVLKKT 130
                                    19        29||      45        63        73        83||     102       112 ||    127   
                                               30|               54|                   84|                 114|          
                                                37                63                    94                  120          


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeeeee...eeeeeee....eeeeeee.eeeeeeeee.....eeeee...eeeeeee..eeeeeee..ee.....hhhh.eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4u3q B  10 KAKAEKVECALKGGIFRGTLPAGIDTTVTFNADGTAQKVELPLTYRGTWMVREDGIVELSLVSKELYELIDSNSVRYMGAPGAGKPSKEMAPFYVLKKT 130
                                    19        29 ||     43        53||      72        82  ||   101       111       121         
                                                31|                54|                   85|                                   
                                                 36                 64                    95
   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 4U3Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U3Q)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

 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 4u3q)
 
  Sites
(no "Sites" information available for 4u3q)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4u3q)
 

(-) 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
  4u3q
    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
  TA17_TREPA | P29722
    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
  TA17_TREPA | P29722
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4U3Q)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4U3Q)