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 PH1033 FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  M. Sugahara, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  12 Jul 04  (Deposition) - 23 Aug 05  (Release) - 26 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Pyrococcus Horikoshii, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugahara, Y. Asada, Y. Morikawa, Y. Kageyama, N. Kunishima
Nucleant-Mediated Protein Crystallization With The Application Of Microporous Synthetic Zeolites.
Acta Crystallogr. , Sect. D V. 64 686 2008
PubMed-ID: 18560157  |  Reference-DOI: 10.1107/S0907444908009980
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0310 PROTEIN PH1033
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 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 1WMM)

(-) Sites  (0, 0)

(no "Site" information available for 1WMM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WMM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WMM)

(-) 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:143
 aligned with Y1033_PYRHO | O58764 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     
          Y1033_PYRHO     1 MTYWICITNRENWEVIKRHNVWGVPKKHKNTLSRVKPGDKLVIYVRQEKDKEGNLLEPKIVGIYEVTSEPYVDFSRIFKPHRGGKETYPYRVKIKPIKIGEINFKPLINDLKFIKNKKRWSMHFFGKAMRELPEEDYKLIEKLLL 145
               SCOP domains d1wmma1 A:1-145 Hypothetical protein PH1033                                                                                                       SCOP domains
               CATH domains 1wmmA00 A:1-145 ph1033 like domains                                                                                                               CATH domains
               Pfam domains -EVE-1wmmA01 A:2-143                                                                                                                           -- Pfam domains
         Sec.struct. author ..eeeeeehhhhhhhhhhhheeeehhhhhhhhh......eeeeee..ee.....ee..eeeeeeee....ee........--.......eeeeeeeeeeeeee.hhhh..........hhhhhh....eeeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wmm A   1 MTYWICITNRENWEVIKRHNVWGVPKKHKNTLSRVKPGDKLVIYVRQEKDKEGNLLEPKIVGIYEVTSEPYVDFSRIFKP--GGKETYPYRVKIKPIKIGEINFKPLINDLKFIKNKKRWSMHFFGKAMRELPEEDYKLIEKLLL 145
                                    10        20        30        40        50        60        70        80  |     90       100       110       120       130       140     
                                                                                                          80 83
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PUA (42)

(-) Gene Ontology  (0, 0)

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

 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 1wmm)
 
  Sites
(no "Sites" information available for 1wmm)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wmm)
 

(-) 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
  1wmm
    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
  Y1033_PYRHO | O58764
    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
  Y1033_PYRHO | O58764
    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
        Y1033_PYRHO | O58764: 2hd9 2zbn

(-) Related Entries Specified in the PDB File

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