Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS YTQB IN COMPLEX WITH SAM
 
Authors :  S. C. Park, W. S. Song, S. I. Yoon
Date :  26 Feb 14  (Deposition) - 02 Apr 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann-Like Fold, A Putative Methyltransferase, S-Adenosyl-L- Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Park, W. S. Song, S. I. Yoon
Structural Analysis Of A Putative Sam-Dependent Methyltransferase, Ytqb, From Bacillus Subtilis
Biochem. Biophys. Res. Commun. V. 446 921 2014
PubMed-ID: 24637210  |  Reference-DOI: 10.1016/J.BBRC.2014.03.026

(-) Compounds

Molecule 1 - PUTATIVE RNA METHYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: A MODIFIED PET49B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BSUW23_14785, YTQB
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SPIZIZENII
    Organism Taxid: 655816
    Strain: ATCC 23059 / NRRL B-14472 / W23

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:27 , THR A:28 , MET A:29 , GLY A:30 , ASN A:31 , GLY A:32 , HIS A:33 , ASP A:34 , ASP A:52 , ILE A:53 , GLN A:54 , SER A:79 , HIS A:80 , ASN A:101 , GLY A:103 , TYR A:104 , LEU A:105 , THR A:113 , THR A:114 , HOH A:401BINDING SITE FOR RESIDUE SAM A 301
2AC2SOFTWAREASN A:45 , ALA B:27 , THR B:28 , MET B:29 , GLY B:30 , ASN B:31 , GLY B:32 , HIS B:33 , ASP B:34 , ASP B:52 , ILE B:53 , GLN B:54 , SER B:79 , HIS B:80 , ASN B:101 , SER B:118 , HOH B:402BINDING SITE FOR RESIDUE SAM B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4POO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4POO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4POO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4POO)

(-) Exons   (0, 0)

(no "Exon" information available for 4POO)

(-) 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:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhhhhhheeeeeeeeeee...hhhhhhhhhhhhhh.....eeeeeeee........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4poo A   6 ILPYSKELLKMAAGEGDIVIDATMGNGHDTQFLAELVGENGHVYAFDIQESAVANTKERLGEAYQARTTLFHKSHDKIAKSLPPETHGKVAAAVFNLGYLPGGDITTNGSSTIKAIEQLLSIMKDEGLIVLVVYHEGKAEKNDVLDFCRNLDQQAARVLTYGFINQQNDPPFIVAIEKKA 190
                                    15        25        35        45        55        65        75        85        95       105   ||  117       127       137    || 150       160       170       180       190
                                                                                                                                 109|                           142|                                            
                                                                                                                                  112                            146                                            


Chain B from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhheeeeeeeeeee..hhhhhhhh.....eeeeeeee........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4poo B   0 PMILKKILPYSKELLKMAAGEGDIVIDATMGNGHDTQFLAELVGENGHVYAFDIQESAVANTKERLGEAYQARTTLFHKSHDKIAKSLPPETHGKVAAAVFNLGSSTIKAIEQLLSIMKDEGLIVLVVYNDVLDFCRNLDQQAARVLTYGFINQQNDPPFIVAIEKKA 190
                                     9        19        29        39        49        59        69        79        89        99  ||   122       132       152       162       172       182        
                                                                                                                                102|                      141|                                      
                                                                                                                                 116                       152
   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 4POO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4POO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4POO)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4poo)
 

(-) 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 | Asym./Biol. Unit - sites 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
  4poo
    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
  E0TY72_BACPZ | E0TY72
    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
  E0TY72_BACPZ | E0TY72
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        E0TY72_BACPZ | E0TY72: 4pon

(-) Related Entries Specified in the PDB File

4pon