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 :  MYCF MYCINAMICIN III 3'-O-METHYLTRANSFERASE IN COMPLEX WITH MG, SAH AND MYCINAMICIN III (SUBSTRATE)
 
Authors :  S. M. Bernard, J. L. Smith
Date :  09 Dec 14  (Deposition) - 04 Mar 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Macrolide, Methyltransferase, Antibiotic, Natural Product, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Bernard, D. L. Akey, A. Tripathi, S. R. Park, J. R. Konwerski, Y. Anzai, S. Li, F. Kato, D. H. Sherman, J. L. Smith
Structural Basis Of Substrate Specificity And Regiochemistr In The Mycf/Tylf Family Of Sugar O-Methyltransferases.
Acs Chem. Biol. V. 10 1340 2015
PubMed-ID: 25692963  |  Reference-DOI: 10.1021/CB5009348

(-) Compounds

Molecule 1 - MYCINAMICIN III 3''-O-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.237
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: MYCF
    Organism Scientific: MICROMONOSPORA GRISEORUBIDA
    Organism Taxid: 28040
    Synonym: MYCINAMICIN BIOSYNTHESIS PROTEIN F

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3ZM32Ligand/IonMYCINAMICIN III

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:189 , ASP A:216 , ASP A:217 , ZM3 A:303 , HOH A:522 , HOH A:545binding site for residue MG A 301
2AC2SOFTWARETHR A:55 , MET A:56 , ILE A:57 , GLU A:83 , GLY A:85 , VAL A:86 , TRP A:87 , ALA A:91 , ASP A:113 , SER A:114 , GLY A:117 , PHE A:118 , LEU A:143 , GLY A:169 , TRP A:170 , PHE A:171 , ASP A:189 , HOH A:507 , HOH A:543 , HOH A:558binding site for residue SAH A 302
3AC3SOFTWAREMET A:56 , LEU A:134 , TYR A:137 , ASP A:191 , ASP A:216 , ASP A:217 , CYS A:219 , GLN A:246 , MG A:301 , HOH A:525 , HOH A:545 , HOH A:569 , HOH A:639binding site for residue ZM3 A 303
4AC4SOFTWAREASP B:189 , ASP B:216 , ASP B:217 , ZM3 B:303 , HOH B:547 , HOH B:566binding site for residue MG B 301
5AC5SOFTWARETHR B:55 , MET B:56 , ILE B:57 , GLU B:83 , GLY B:85 , VAL B:86 , TRP B:87 , ALA B:91 , ASP B:113 , SER B:114 , GLY B:117 , PHE B:118 , GLY B:169 , TRP B:170 , PHE B:171 , ASP B:189 , HOH B:505 , HOH B:530 , HOH B:534binding site for residue SAH B 302
6AC6SOFTWAREHOH A:475 , TYR B:49 , MET B:56 , LEU B:134 , TYR B:137 , ASP B:191 , ASP B:216 , ASP B:217 , CYS B:219 , GLN B:246 , MG B:301 , HOH B:516 , HOH B:566 , HOH B:568binding site for residue ZM3 B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X7U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X7U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X7U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X7U)

(-) Exons   (0, 0)

(no "Exon" information available for 4X7U)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...................hhhhhhh...........hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh......eeeee............hhhhhhhhhhhhh.......hhhhhhhhhhhh......eeeee.hhhhhh.......eeeeee...hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh.....ee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4x7u A   3 PSTGVELYLDLLKRTVSNFIYQDATHVAGLITEAAFVEEARESGEDYPTVAHTMIGMKRLNNLQHCVESALRDGVPGDVLETGVWRGGACIFARGILKAYDVRDRTVWVADSFQGFPKITDDDHPMDAEMNLHQYNEAVDLPTSLATVQRNFSRYGLLDDQVRFLPGWFKDTMPTAPFERLAVLRMDGDSYGATMDVLTHAYPRLSPGGFAIIDDYCIPACREAVHEYRDRHGISDEIVEIDRQGVYWRRSA 254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  


Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...................hhhhhhh...........hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh......eeeee............hhhhhhhhhhhhh.......hhhhhhhhhhhh......eeeee.hhhhhh.......eeeeee...hhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhh.....ee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4x7u B   3 PSTGVELYLDLLKRTVSNFIYQDATHVAGLITEAAFVEEARESGEDYPTVAHTMIGMKRLNNLQHCVESALRDGVPGDVLETGVWRGGACIFARGILKAYDVRDRTVWVADSFQGFPKITDDDHPMDAEMNLHQYNEAVDLPTSLATVQRNFSRYGLLDDQVRFLPGWFKDTMPTAPFERLAVLRMDGDSYGATMDVLTHAYPRLSPGGFAIIDDYCIPACREAVHEYRDRHGISDEIVEIDRQGVYWRRSA 254
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   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 4X7U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X7U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X7U)

(-) Gene Ontology  (7, 7)

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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZM3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4x7u)
 

(-) 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
  4x7u
    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
  MYCF_MICGR | Q49492
    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)
  2.1.1.237
    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
  MYCF_MICGR | Q49492
    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
        MYCF_MICGR | Q49492: 4x7v 4x7w 4x7x 4x7y 4x7z 4x81 4xvy 4xvz

(-) Related Entries Specified in the PDB File

4x7v 4x7w 4x7x 4x7y 4x7z 4x81