Show PDB file:   
         Plain Text   HTML   (compressed file size)
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Authors :  G. Hu, A. E. Hodel, P. D. Gershon, F. A. Quiocho
Date :  12 Jul 98  (Deposition) - 22 Jul 99  (Release) - 24 Feb 09  (Revision)
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Methylated Adenine, Methyltransferase, Rna Cap Analog, Poly (A) Polymerase, Vaccinia, Mrna Processing, Transcription, Complex (Transferase/Rna Cap Analog) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  G. Hu, P. D. Gershon, A. E. Hodel, F. A. Quiocho
Mrna Cap Recognition: Dominant Role Of Enhanced Stacking Interactions Between Methylated Bases And Protein Aromatic Side Chains.
Proc. Natl. Acad. Sci. Usa V. 96 7149 1999
PubMed-ID: 10377383  |  Reference-DOI: 10.1073/PNAS.96.13.7149
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VP39
    EC Number2.7.7.19
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Organism ScientificVACCINIA VIRUS
    Organism Taxid10245

 Structural Features

(-) Chains, Units

Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
1AC1SOFTWAREGLN A:39 , LEU A:42 , TYR A:66 , ILE A:67 , GLY A:68 , SER A:69 , ALA A:70 , PRO A:71 , GLY A:72 , HIS A:74 , ASP A:95 , ARG A:97 , PHE A:115 , VAL A:116 , ASP A:138 , VAL A:139 , ARG A:140 , HOH A:707 , HOH A:708BINDING SITE FOR RESIDUE SAH A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MAG)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
1Ala A:70 -Pro A:71
2His A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
1SAM_MT_2O_PKPS51612 Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC family profile.MCE_VACCW4-262  1A:4-262
Biological Unit 1 (1, 2)
1SAM_MT_2O_PKPS51612 Poxvirus/kinetoplastid-type ribose 2'-O-methyltransferase (EC family profile.MCE_VACCW4-262  2A:4-262

(-) Exons   (0, 0)

(no "Exon" information available for 3MAG)

(-) Sequences/Alignments

Asymmetric 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:291
 aligned with MCE_VACCW | P07617 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
               SCOP domains d3maga_ A: Polymerase regulatory subunit VP39                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3magA00 A:1-297 Vaccinia Virus protein VP39                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh........hhhhh........hhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh....eeeeee.....hhh.....eeeee....hhhhhhhhhhh....eeeee....------..hhhhhhhhhhhhhhhhhh...eeeeee....hhh....eeee..eee...........eeeeee.......eeee.hhhhhhhhhhhhhhhh.hhh............hhhhhhhhhhhh.........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_MT_2O_PK  PDB: A:4-262 UniProt: 4-262                                                                                                                                                                                                                          ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
                                                                                                                                                                      141    148                                                                                                                                                     

   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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (MCE_VACCW | P07617)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004483    mRNA (nucleoside-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA. R may be guanosine or adenosine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0080009    mRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an mRNA molecule.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031440    regulation of mRNA 3'-end processing    Any process that modulates the frequency, rate or extent of mRNA 3'-end processing, any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.


(-) Interactive Views

Asymmetric 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)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(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
    3MA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
  Cis Peptide Bonds
    Ala A:70 - Pro A:71   [ RasMol ]  
    His A:129 - Pro A:130   [ RasMol ]  
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
Access by UniProt ID/Accession number
  MCE_VACCW | P07617
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
Access by Enzyme Classificator   (EC Number)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
Access by UniProt ID/Accession number
  MCE_VACCW | P07617
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        MCE_VACCW | P076171av6 1b42 1bky 1eam 1eqa 1jsz 1jte 1jtf 1p39 1v39 1vp3 1vp9 1vpt 2ga9 2gaf 2vp3 3er8 3er9 3erc 3mct 4dcg

(-) Related Entries Specified in the PDB File

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