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

(-) Description

Title :  THEORITICAL MODEL OF HYPOTHETICAL PROTIEN
 
Authors :  K. Siddhartha, A. Jayasri
Date :  20 Aug 02  (Deposition) - 04 Sep 02  (Release) - 04 Sep 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Hypothetical Protein, Complete Proteome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Siddhartha, A. Jayasri
Theoritical Model Of Hypothetical Protien
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN HP0162
    Chains: A
    Organism Common: BACTERIA
    Organism Scientific: HELICOBACTER PYLORI

 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 1MHF)

(-) Sites  (0, 0)

(no "Site" information available for 1MHF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ala A:71 -Ser A:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MHF)

(-) Exons   (0, 0)

(no "Exon" information available for 1MHF)

(-) 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:240
 aligned with Y162_HELPY | O24970 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           Y162_HELPY     1 MGRAFEYRRAAKEKRWDKMSKVFPKLAKAITLAAKDGGSEPDTNAKLRTAILNAKAQNMPKDNIDAAIKRASSKEGNLSEITYEGKANFGVLIIMECMTDNPTRTIANLKSYFNKTQGASIVPNGSLEFMFNRKSVFECLKNEVENLKLSLEDLEFALIDYGLEELEEVEDKIIIRGDYNSFKLLNEGFESLKLPILKASLQRIATTPIELNDEQMELTEKLLDRIEDDDDVVALYTNIE 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhh........eeeeeeeeehhheeeeeeeee.hhhhhhhhhhhhhhh....ee....hhhhhh...eeeeee....hhhhhhhhhhhhh..eee.....eeeeeehhhhhhhhhhhhhh......eee...............hhhhhhhhhhhhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mhf A   1 MGRAFEYRRAAKEKRWDKMSKVFPKLAKAITLAAKDGGSEPDTNAKLRTAILNAKAQNMPKDNIDAAIKRASSKEGNLSEITYEGKANFGVLIIMECMTDNPTRTIANLKSYFNKTQGASIVPNGSLEFMFNRKSVFECLKNEVENLKLSLEDLEFALIDYGLEELEEVEDKIIIRGDYNSFKLLNEGFESLKLPILKASLQRIATTPIELNDEQMELTEKLLDRIEDDDDVVALYTNIE 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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 1MHF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Theoretical Model(hide GO term definitions)
Chain A   (Y162_HELPY | O24970)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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 1mhf)
 
  Sites
(no "Sites" information available for 1mhf)
 
  Cis Peptide Bonds
    Ala A:71 - Ser A:72   [ 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
  1mhf
    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
  Y162_HELPY | O24970
    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
  Y162_HELPY | O24970
    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
        Y162_HELPY | O24970: 1mw7

(-) Related Entries Specified in the PDB File

1kon 1KON CONTAINS E.COLI YEBC
1lfp 1LFP CONTAINS A CONSERVED HYPOTHETICAL PROTEIN AQ1575