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 THE DUF16 DOMAIN OF MPN010 FROM MYCOPLASMA PNEUMONIAE
 
Authors :  D. H. Shin, J. -S. Kim, H. Yokota, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date :  13 Oct 05  (Deposition) - 07 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Duf16, Mpn010, Hypothetical Protein, Coiled-Coil, Stutter, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, J. -S. Kim, H. Yokota, R. Kim, S. -H. Kim
Crystal Structure Of The Duf16 Domain Of Mpn010 From Mycoplasma Pneumoniae.
Protein Sci. V. 15 921 2006
PubMed-ID: 16522803  |  Reference-DOI: 10.1110/PS.051993506
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0134 PROTEIN MPN010
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PB3, PET21A DERIVED
    Expression System Strain: B834(DE3), PSJS1244
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DUF16 DOMAIN, RESIDUES 46-130
    Organism Scientific: MYCOPLASMA PNEUMONIAE
    Organism Taxid: 2104
    Synonym: D12_ORF131

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2BA2)

(-) Sites  (0, 0)

(no "Site" information available for 2BA2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BA2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BA2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BA2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BA2)

(-) Exons   (0, 0)

(no "Exon" information available for 2BA2)

(-) 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:81
 aligned with Y010_MYCPN | P75103 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:81
                                    59        69        79        89        99       109       119       129 
           Y010_MYCPN    50 GTRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLES 130
               SCOP domains d2ba2a1 A:5-85 Hypothetical protein MPN010                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2ba2 A   5 GTRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLES  85
                                    14        24        34        44        54        64        74        84 


Chain B from PDB  Type:PROTEIN  Length:80
 aligned with Y010_MYCPN | P75103 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:80
                                    60        70        80        90       100       110       120       130
           Y010_MYCPN    51 TRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLES 130
               SCOP domains d2ba2b_ B: Hypothetical protein MPN010                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 2ba2 B 106 TRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLES 185
                                   115       125       135       145       155       165       175       185


Chain C from PDB  Type:PROTEIN  Length:81
 aligned with Y010_MYCPN | P75103 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:81
                                    59        69        79        89        99       109       119       129 
           Y010_MYCPN    50 GTRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLES 130
               SCOP domains d2ba2c_ C: Hypothetical protein MPN010                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2ba2 C 205 GTRYVTHKQLDEKLKNFVTKTEFKEFQTVVMESFAVQNQNIDAQGEQIKELQVEQKAQGKTLQLILEALQGINKRLDNLES 285
                                   214       224       234       244       254       264       274       284
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BA2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BA2)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2BA2)

 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 2ba2)
 
  Sites
(no "Sites" information available for 2ba2)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ba2)
 

(-) 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
  2ba2
    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
  Y010_MYCPN | P75103
    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
  Y010_MYCPN | P75103
    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 2BA2)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2BA2)