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 AN HYPOTHETICAL PROTEIN
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Park, K. Gajiwala, G. Eroshkina, E. Furlong, D. He, Y. Batiyenko, R. Romero, J. Christopher, J. Badger, J. Hendle, J. Lin, T. Peat, S. Buchanan
Crystal Structure Of Yigz, A Conserved Hypothetical Protein From Escherichia Coli K12 With A Novel Fold
Proteins V. 55 775 2004
PubMed-ID: 15103642  |  Reference-DOI: 10.1002/PROT.20087
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YIGZ
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YIGZ, B3848
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1VI7)

(-) Sites  (0, 0)

(no "Site" information available for 1VI7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VI7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:63 -Pro A:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VI7)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPF0029PS00910 Uncharacterized protein family UPF0029 signature.YIGZ_ECOLI80-109  1A:83-112

(-) Exons   (0, 0)

(no "Exon" information available for 1VI7)

(-) 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:206
 aligned with YIGZ_ECOLI | P27862 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:206
                             1                                                                                                                                                                                                        204 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199    | 
           YIGZ_ECOLI     - -MESWLIPAAPVTVVEEIKKSRFITMLAHTDGVEAAKAFVESVRAEHPDARHHCVAWVAGAPDDSQQLGFSDDGEPAGTAGKPMLAQLMGSGVGEITAVVVRYYGGILLGTGGLVKAYGGGVNQALRQLTTQRKTPLTEYTLQCEYHQLTGIEALLGQCDGKIINSDYQAFVLLRVALPAAKVAEFSAKLADFSRGSLQLLAIEE-   -
               SCOP domains d1vi7a1 A:3-137 Hypothetical protein YigZ, N-terminal domain                                                                           d1vi7a2 A:138-208 Hypothetical protein YigZ, C-terminal domain          SCOP domains
               CATH domains 1vi7A01 A:3-137 Hypothetical protein yigz, domain 1                                                                                    1vi7A02 A:138-208  [code=3.30.70.240, no name defined]                  CATH domains
               Pfam domains -----------------UPF0029-1vi7A02 A:20-129                                                                                      --------------DUF1949-1vi7A01 A:144-199                               --------- Pfam domains
         Sec.struct. author ....eeee...eeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhh.......eeee..........eee.........hhhhhhhhhhhh...eeee..ee......hhhhhhhhhhhhhhhhhh...eeee...eeeeeee...hhhhhhhhhhhh..eeeeeee...eeeeeee...hhhhhhhhhhhhh......ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------UPF0029  PDB: A:83-112        ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi7 A   3 LMESWLIPAAPVTVVEEIKKSRFITMLAHTDGVEAAKAFVESVRAEHPDARHHCVAWVAGAPDDSQQLGFSDDGEPAGTAGKPMLAQLMGSGVGEITAVVVRYYGGILLGTGGLVKAYGGGVNQALRQLTTQRKTPLTEYTLQCEYHQLTGIEALLGQCDGKIINSDYQAFVLLRVALPAAKVAEFSAKLADFSRGSLQLLAIEEE 208
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: EF-G_C (20)
(-)
Clan: S5 (103)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1VI7)

 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 1vi7)
 
  Sites
(no "Sites" information available for 1vi7)
 
  Cis Peptide Bonds
    Ala A:63 - Pro A:64   [ RasMol ]  
 

(-) 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
  1vi7
    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
  YIGZ_ECOLI | P27862
    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
  YIGZ_ECOLI | P27862
    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 1VI7)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VI7)