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

(-) Description

Title :  CRYSTAL STRUCTURE OF MEDICAGO TRUNCATULA UGT85H2- INSIGHTS INTO THE STRUCTURAL BASIS OF A MULTIFUNCTIONAL (ISO) FLAVONOID GLYCOSYLTRANSFERASE
 
Authors :  L. Li, L. V. Modolo, L. L. Escamilla-Trevino, X. Wang
Date :  01 May 07  (Deposition) - 10 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosylation, Isoflavonoid, Crystal Structure, Uridine Diphosphate Glycosyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Li, L. V. Modolo, L. L. Escamilla-Trevino, L. Achnine, R. A. Dixon, X. Wang
Crystal Structure Of Medicago Truncatula Ugt85H2 - Insights Into The Structural Basis Of A Multifunctional (Iso)Flavonoid Glycosyltransferase.
J. Mol. Biol. V. 370 951 2007
PubMed-ID: 17553523  |  Reference-DOI: 10.1016/J.JMB.2007.05.036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-GLUCURONOSYL/UDP-GLUCOSYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Common: BARREL MEDIC
    Organism Scientific: MEDICAGO TRUNCATULA
    Organism Taxid: 3880

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2PQ6)

(-) Sites  (0, 0)

(no "Site" information available for 2PQ6)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:379 -A:396

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:168 -Pro A:169
2Gly A:256 -Pro A:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PQ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PQ6)

(-) Exons   (0, 0)

(no "Exon" information available for 2PQ6)

(-) 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:443
 aligned with A6XNC5_MEDTR | A6XNC5 from UniProtKB/TrEMBL  Length:482

    Alignment length:473
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477   
         A6XNC5_MEDTR     8 KPHVVMIPYPVQGHINPLFKLAKLLHLRGFHITFVNTEYNHKRLLKSRGPKAFDGFTDFNFESIPDGLTPMEGDGDVSQDVPTLCQSVRKNFLKPYCELLTRLNHSTNVPPVTCLVSDCCMSFTIQAAEEFELPNVLYFSSSACSLLNVMHFRSFVERGIIPFKDESYLTNGCLETKVDWIPGLKNFRLKDIVDFIRTTNPNDIMLEFFIEVADRVNKDTTILLNTFNELESDVINALSSTIPSIYPIGPLPSLLKQTPQIHQLDSLDSNLWKEDTECLDWLESKEPGSVVYVNFGSITVMTPEQLLEFAWGLANCKKSFLWIIRPDLVIGGSVIFSSEFTNEIADRGLIASWCPQDKVLNHPSIGGFLTHCGWNSTTESICAGVPMLCWPFFADQPTDCRFICNEWEIGMEIDTNVKREELAKLINEVIAGDKGKKMKQKAMELKKKAEENTRPGGCSYMNLNKVIKDVLLK 480
               SCOP domains d2pq6a1 A:8-480 (Iso)flavonoid glycosyltransf            erase                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------UDPGT-2pq6A01 A:28-459                                                                                                                                                                                                                                                                                                                                                                                                                          --------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhh------------.eeeeee.....---------.hhhhhhhhhh..hhhhhhhhhhhhhh........eeeee...hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh......hhhhhh.hhhhh...........hhhhhhhhhh.....hhhhhhhhhhhhh......eee..hhhhhhhhhhhhhh....eee..hhhhhhhh..hhhhhh.---------hhhhhhhh......eeeee.......hhhhhhhhhhhhhhh..eeeee.hhhhh..hhhhhhhhhhhhhh..eeee...hhhhhhh...eeeeee..hhhhhhhhhhhh..eee.....hhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pq6 A   8 KPHVVMIPYPVQGHINPLFKLAKLLHLRGFHITFVNTEYNHKRLL------------DFNFESIPDGLT---------QDVPTLCQSVRKNFLKPYCELLTRLNHSTNVPPVTCLVSDCCMSFTIQAAEEFELPNVLYFSSSACSLLNVMHFRSFVERGIIPFKDESYLTNGCLETKVDWIPGLKNFRLKDIVDFIRTTNPNDIMLEFFIEVADRVNKDTTILLNTFNELESDVINALSSTIPSIYPIGPLPSLLKQTPQIHQLDS---------TECLDWLESKEPGSVVYVNFGSTTVMTPEQLLEFAWGLANCKKSFLWIIRPDLVIGGSVIFSSEFTNEIADRGLIASWCPQDKVLNHPSIGGFLTHCGWNSTTESICAGVPMLCWPFFADQPTDCRFICNEWEIGMEIDTNVKREELAKLINEVIAGDKGKKMKQKAMELKKKAEENTRPGGCSYMNLNKVIKDVLLK 480
                                    17        27        37        47    |    -       |67        |-        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267     |   -     | 287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477   
                                                                       52           65         76        86                                                                                                                                                                                        273       283
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PQ6)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GT-B (132)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6XNC5_MEDTR | A6XNC5)
molecular function
    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).
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

 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 2pq6)
 
  Sites
(no "Sites" information available for 2pq6)
 
  Cis Peptide Bonds
    Gly A:256 - Pro A:257   [ RasMol ]  
    Ile A:168 - Pro A:169   [ 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 ](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
  2pq6
    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
  A6XNC5_MEDTR | A6XNC5
    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
  A6XNC5_MEDTR | A6XNC5
    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 2PQ6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PQ6)