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 ANTIFREEZE PROTEIN FROM AN ANTARCTIC SEA ICE BACTERIUM COLWELLIA SP.
 
Authors :  Y. Hanada, Y. Nishimiya, A. Miura, S. Tsuda, H. Kondo
Date :  10 Jan 14  (Deposition) - 02 Jul 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Right-Handed Beta-Helix, Antifreeze Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hanada, Y. Nishimiya, A. Miura, S. Tsuda, H. Kondo
Hyperactive Antifreeze Protein From An Antarctic Sea Ice Bacterium Colwellia Sp. Has A Compound Ice-Binding Site Without Repetitive Sequences
Febs J. 2014
PubMed-ID: 24938370  |  Reference-DOI: 10.1111/FEBS.12878

(-) Compounds

Molecule 1 - ICE-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 28-253
    Organism Scientific: COLWELLIA
    Organism Taxid: 397414
    Strain: SLW05
    Synonym: ANTIFREEZE PROTEIN

 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 3WP9)

(-) Sites  (0, 0)

(no "Site" information available for 3WP9)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:48 -A:66

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:26 -Pro A:27
2Ser A:37 -Pro A:38
3Leu A:64 -Pro A:65
4Val A:92 -Pro A:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WP9)

(-) Exons   (0, 0)

(no "Exon" information available for 3WP9)

(-) 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:224
 aligned with A5XB26_9GAMM | A5XB26 from UniProtKB/TrEMBL  Length:253

    Alignment length:224
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247    
         A5XB26_9GAMM    28 AGPYAVELGEAGTFTILSKSGITDVYPSTVTGNVGTSPITGAALLLNCDEVTGAMYTVDSAGPLPCSINSPYLLELAVSDMGIAYNDAAGRVPADHTELGTGEIGGLTLEPGVYKWSSDVNISTDVTFNGTMDDVWIMQISGNLNQANAKRVTLTGGALAKNIFWQVAGYTALGTYASFEGIVLSKTLISVNTGTTVNGRLLAQTAVTLQKNTINAPTEQYEEA 251
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.eeeee...eeee...eee.eeee...hhhhh..hhhhh...eee.........eeehhhhhhhhhhhhhhhhhhhhh.....ee.hhhhh....ee..eeeee...eee...eeee......eeeee...eee.....eeee...hhh.eeeee...eee....eeeeeeee...eee....eeeeeeee...eeee..eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wp9 A   1 AGPYAVELGEAGTFTILSKSGITDVYPSTVTGNVGTSPITGAALLLNCDEVTGAMYTVDSAGPLPCSINSPYLLELAVSDMGIAYNDAAGRVPADHTELGTGEIGGLTLEPGVYKWSSDVNISTDVTFNGTMDDVWIMQISGNLNQANAKRVTLTGGALAKNIFWQVAGYTALGTYASFEGIVLSKTLISVNTGTTVNGRLLAQTAVTLQKNTINAPTEQYEEA 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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 3WP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WP9)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3WP9)

 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 3wp9)
 
  Sites
(no "Sites" information available for 3wp9)
 
  Cis Peptide Bonds
    Leu A:64 - Pro A:65   [ RasMol ]  
    Ser A:37 - Pro A:38   [ RasMol ]  
    Tyr A:26 - Pro A:27   [ RasMol ]  
    Val A:92 - Pro A:93   [ 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
  3wp9
    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
  A5XB26_9GAMM | A5XB26
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  A5XB26_9GAMM | A5XB26
    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 3WP9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3WP9)