Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theor.Model - manually
(-)Theoretical Model
collapse expand < >
Image Theor.Model - manually
Theor.Model - manually  (Jmol Viewer)
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  TETRATRICOPEPTIDE REPEATS IN TYPE III SECRETION CHAPERONES AND REGULATORS
 
Authors :  M. J. Pallen, M. S. Francis, K. Futterer
Date :  04 Mar 03  (Deposition) - 15 Jul 03  (Release) - 15 Jul 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B
Keywords :  Type-Iii-Secretion, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Pallen, M. S. Francis, K. Futterer
Tetratricopeptide-Like Repeats In Type-Iii-Secretion Chaperones And Regulators
Fems Microbiol. Lett. V. 223 53 2003
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LOW CALCIUM RESPONSE LOCUS PROTEIN H
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
 
Molecule 2 - YOPD PROTEIN
    Chains: B
    Organism Common: BACTERIA
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1OOS)

(-) Sites  (0, 0)

(no "Site" information available for 1OOS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OOS)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ser A:32 -Ser A:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OOS)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPR_REGIONPS50293 TPR repeat region circular profile.LCRH_YERPS36-137  1A:36-137

(-) Exons   (0, 0)

(no "Exon" information available for 1OOS)

(-) Sequences/Alignments

Theoretical Model
   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:134
 aligned with LCRH_YERPS | P23995 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:134
                                    41        51        61        71        81        91       101       111       121       131       141       151       161    
           LCRH_YERPS    32 SSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIADKPEFKELSTRVSSMLEAIKLKKEMEHECV 165
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----TPR_REGION  PDB: A:36-137 UniProt: 36-137                                                             ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oos A  32 SSDTLEQLYSLAFNQYQSGKYEDAHKVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAIMDIKEPRFPFHAAECLLQKGELAEAESGLFLAQELIADKPEFKELSTRVSSMLEAIKLKKEMEHECV 165
                                    41        51        61        71        81        91       101       111       121       131       141       151       161    


Chain B from PDB  Type:PROTEIN  Length:23
 aligned with YOPD_YERPS | Q06131 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:23
                                   287       297   
           YOPD_YERPS   278 DNFMKDVLRLIEQYVSSHTHAMK 300
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 1oos B 278 DNFMKDVLRLIEQYVSSHTHAMK 300
                                   287       297
   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 1OOS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OOS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OOS)

(-) Gene Ontology  (1, 1)

Theoretical Model(hide GO term definitions)
Chain A   (LCRH_YERPS | P23995)
biological process
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

Chain B   (YOPD_YERPS | Q06131)

 Visualization

(-) Interactive Views

Theoretical Model
  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 1oos)
 
  Sites
(no "Sites" information available for 1oos)
 
  Cis Peptide Bonds
    Ser A:32 - Ser A:33   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model 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
  1oos
    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
  LCRH_YERPS | P23995
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  YOPD_YERPS | Q06131
    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
  LCRH_YERPS | P23995
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  YOPD_YERPS | Q06131
    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
        LCRH_YERPS | P23995: 1ool
        YOPD_YERPS | Q06131: 1kdl

(-) Related Entries Specified in the PDB File

1ool 1oom 1ooo 1oor