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 :  MOLECULAR DYNAMICS ANALYSIS OF OVINE AND BOVINE ISG15
 
Authors :  S. Nelson, C. M. Sorensen, T. R. Hansen
Date :  19 Jul 05  (Deposition) - 15 Nov 06  (Release) - 15 Nov 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Ubiquitin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Sorensen, L. A. Rempel, B. R. Francis, D. J. Perry, S. Nelson, R. V. Lewis, A. L. Haas, T. R. Hansen
The Hinge Region Between Two Ubiquitin-Like Domains Destabilizes Recombinant Isg15 In Solution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN CROSS-REACTIVE PROTEIN
    Chains: A
    Engineered: YES
    Synonym: BOVINE ISG15
    Synthetic: YES

 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 2BX0)

(-) Sites  (0, 0)

(no "Site" information available for 2BX0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BX0)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Ala A:46 -His A:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BX0)

(-) PROSITE Motifs  (1, 2)

Theoretical Model (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBIQUITIN_2PS50053 Ubiquitin domain profile.ISG15_BOVIN3-76
79-154		  2A:3-76
A:79-149

(-) Exons   (2, 2)

Theoretical Model (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000195731ENSBTAE00000159221chr16:48719832-4871976073ISG15_BOVIN1-111A:1-11
1.2ENSBTAT000000195732ENSBTAE00000159222chr16:48719322-48718794529ISG15_BOVIN2-1541531A:2-149148

(-) 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:149
 aligned with ISG15_BOVIN | O02741 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140         
          ISG15_BOVIN     1 MGGDLTVKMLGGQEILVPLRDSMTVSELKQFIAQKINVPAFQQRLAHLDSREVLQEGVPLVLQGLRAGSTVLLVVQNCISILVRNDKGRSSPYEVQLKQTVAELKQQVCQKERVQADQFWLSFEGRPMDDEHPLEEYGLMKGCTVFMNL 149
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eeee.........hhhhhhhhhhhh.hhh.eeeee...........hhhhhhh.....eeeee...eeeee.......eeeee........hhhhhhhhh.............................ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --UBIQUITIN_2  PDB: A:3-76 UniProt: 3-76                                    --UBIQUITIN_2  PDB: A:79-149 UniProt: 79-154                              PROSITE
               Transcript 1 1Exon 1.2  PDB: A:2-149 UniProt: 2-154 [INCOMPLETE]                                                                                                   Transcript 1
                 2bx0 A   1 MGGDLTVKMLGGQEILVPLRDSMTVSELKQFIAQKINVPAFQQRLAHLDSREVLQEGVPLVLQGLRAGSTVLLVVQNCISILVRNDKGRSSPYEVQLKQTVAELKQQVCQKERVQADQFWLSFEGRPMDDEHPLEEYGLMKGCTVFMNL 149
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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 2BX0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BX0)

(-) Gene Ontology  (12, 12)

Theoretical Model(hide GO term definitions)
Chain A   (ISG15_BOVIN | O02741)
molecular function
    GO:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
    GO:0032020    ISG15-protein conjugation    The covalent addition to a protein of ISG15, a ubiquitin-like protein.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0019941    modification-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent modification of the target protein.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0032649    regulation of interferon-gamma production    Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0034340    response to type I interferon    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 type I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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 2bx0)
 
  Sites
(no "Sites" information available for 2bx0)
 
  Cis Peptide Bonds
    Ala A:46 - His A:47   [ 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
  2bx0
    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
  ISG15_BOVIN | O02741
    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
  ISG15_BOVIN | O02741
    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 2BX0)

(-) Related Entries Specified in the PDB File

2bx0 MOLECULAR DYNAMICS ANALYSIS OF OVINE AND BOVINE ISG15
2bx1 MOLECULAR DYNAMICS ANALYSIS OF OVINE AND BOVINE ISG15