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 :  CRYSTAL STRUCTURE OF A GLYCOSYLTRANSFERASE INVOLVED IN THE GLYCOSYLATION OF THE MAJOR CAPSID OF PBCV-1
 
Authors :  Y. Zhang, Y. Xiang, J. L. Van Etten, M. G. Rossmann
Date :  19 Mar 07  (Deposition) - 21 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyltransferase, Pbcv-1 A64R, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, Y. Xiang, J. L. Van Etten, M. G. Rossmann
Structure And Function Of A Chlorella Virus-Encoded Glycosyltransferase.
Structure V. 15 1031 2007
PubMed-ID: 17850743  |  Reference-DOI: 10.1016/J.STR.2007.07.006

(-) Compounds

Molecule 1 - PUTATIVE GLYCOSYLTRANSFERASE (MANNOSYLTRANSFERASE) INVOLVED IN GLYCOSYLATING THE PBCV-1 MAJOR CAPSID PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB-1
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FRAGMENT
    Gene: A64R
    Organism Scientific: PARAMECIUM BURSARIA CHLORELLA VIRUS 1
    Organism Taxid: 10506
    Synonym: VP54

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:78 , ASP A:80 , HIS A:193 , UDP A:411BINDING SITE FOR RESIDUE MN A 214
2AC2SOFTWAREGLY A:11 , HIS A:12 , PHE A:13 , LEU A:53 , HIS A:54 , ARG A:57 , TRP A:76 , ASP A:78 , SER A:79 , ASP A:80 , HIS A:193 , CYS A:195 , GLY A:196 , ARG A:202 , MN A:214BINDING SITE FOR RESIDUE UDP A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P73)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:13 -Pro A:14
2Ala A:111 -Pro A:112
3Ala A:143 -Pro A:144
4Phe A:148 -Pro A:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P73)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P73)

(-) Exons   (0, 0)

(no "Exon" information available for 2P73)

(-) 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:207
 aligned with Q89399_PBCV1 | Q89399 from UniProtKB/TrEMBL  Length:638

    Alignment length:207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       
         Q89399_PBCV1     3 TPCITILSGHFPKETIYARKTKELVEEYCSIHGYNFYYEESEPLETEEHALHFRRSWIIQQAAEKFPSTEWFLWLDSDVYVNPKNKNKPITSFIDLSDPNILYHTFHEAPWGSYPINTGVKFVHKDALEIEKIVWSLRNEAPWNTFPYEQKTVYEYVFPRIPGRYIVHDPYTLNCIVKAYPEHVKDALFVHMCGTSRAERDEHMEMV 209
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Glyco_transf_34-2p73A01 A:11-106                                                                ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhh....eeeee...eee.......hhhhh.........eeee.............eeeee..hhhhhhhhhhh..........hhhhhhhhhhhhhh...eeee......ee......hhhhh.eee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p73 A   3 TPCITILSGHFPKETIYARKTKELVEEYCSIHGYNFYYEESEPLETEEHALHFRRSWIIQQAAEKFPSTEWFLWLDSDVYVNPKNKNKPITSFIDLSDPNILYHTFHEAPWGSYPINTGVKFVHKDALEIEKIVWSLRNEAPWNTFPYEQKTVYEYVFPRIPGRYIVHDPYTLNCIVKAYPEHVKDALFVHMCGTSRAERDEHMEMV 209
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   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 2P73)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P73)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q89399_PBCV1 | Q89399)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

 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
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:111 - Pro A:112   [ RasMol ]  
    Ala A:143 - Pro A:144   [ RasMol ]  
    Phe A:13 - Pro A:14   [ RasMol ]  
    Phe A:148 - Pro A:149   [ RasMol ]  
 

(-) 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
  2p73
    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
  Q89399_PBCV1 | Q89399
    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
  Q89399_PBCV1 | Q89399
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q89399_PBCV1 | Q89399: 2p6w 2p72

(-) Related Entries Specified in the PDB File

2p6w 2p72