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 :  PROTEIN STRUCTURE OF USP FROM L. MAJOR BOUND TO URIDINE-5'-DIPHOSPHATE GLUCOSE
 
Authors :  A. Dickmanns, S. Damerow, P. Neumann, E. -C. Schulz, A. Lamerz, F. H. Rou R. Ficner
Date :  17 Aug 10  (Deposition) - 17 Nov 10  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Left Handed Beta Helix, Rossmann Fold, Udp Sugar Pyrophosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Dickmanns, S. Damerow, P. Neumann, E. C. Schulz, A. C. Lamerz, F. H. Routier, R. Ficner
Structural Basis For The Broad Substrate Range Of The Udp-Sugar Pyrophosphorylase From Leishmania Major.
J. Mol. Biol. V. 405 461 2011
PubMed-ID: 21073876  |  Reference-DOI: 10.1016/J.JMB.2010.10.057

(-) Compounds

Molecule 1 - UDP-SUGAR PYROPHOSPHORYLASE
    Chains: A
    EC Number: 2.7.7.64
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: USP
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: 5ASKH

 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
1GOL1Ligand/IonGLYCEROL
2UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:120 , ALA A:121 , GLY A:122 , GLY A:123 , MET A:168 , GLN A:196 , PRO A:221 , GLY A:223 , HIS A:224 , GLN A:270 , ASP A:271 , ILE A:307 , GLY A:308 , ASN A:325 , GLU A:327 , TYR A:328 , SER A:358 , VAL A:359 , ASN A:360 , GLN A:407 , TYR A:430 , LYS A:434 , HOH A:697 , HOH A:721 , HOH A:752BINDING SITE FOR RESIDUE UPG A 7566
2AC2SOFTWARESER A:478 , SER A:479 , GLN A:480 , THR A:603BINDING SITE FOR RESIDUE GOL A 642

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OH4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:495 -Pro A:496

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OH4)

(-) Exons   (0, 0)

(no "Exon" information available for 3OH4)

(-) 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:585
 aligned with D3G6S4_LEIMA | D3G6S4 from UniProtKB/TrEMBL  Length:630

    Alignment length:608
                                    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       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602        
         D3G6S4_LEIMA     3 NPSNSNLQALREELCTPGLDQGHLFEGWPETVDECNERQIALLTDLYMFSNMYPGGVAQYIRNGHELLARESEEVDFAALEMPPLIFEAPSLHRRTAERTALENAGTAMLCKTVFVLVAGGLGERLGYSSIKVSLPVETATNTTYLAYYLRWAQRVGGKEVPFVIMTSDDTHDRTLQLLRELQLEVPNLHVLKQGQVFCFADSAAHLALDETGKLLRKPHGHGDVHSLIYNATVKRDVVPDSGDGTATAQPLVNDWLAAGYESIVFIQDTNAGATITIPISLALSAEHSLDMNFTCIPRVPKEPIGLLCRTKKNSGDPWLVANVEYNVFAEVSRALNKDGGDEVSDPTGFSPFPGSVNTLVFKLSSYVDRLRESHGIVPEFINPKYSDETRRSFKKPARIESLMQDIALLFSEDDYRVGGTVFERFSYQPVKNSLEEAAGLVAQGNGAYCAATGEAAFYELQRRRLKAIGLPLFYSSQPEVTVAKDAFGVRLFPIIVLDTVCASSGSLDDLARVFPTPEKVHIDQHSTLIVEGRVIIESLELYGALTIRGPTDSMALPHVVRNAVVRNAGWSVHAILSLCAGRDSRLSEVDRIRGFVLKKTAMAVMDC 610
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------UDPGP-3oh4A01 A:60-236                                                                                                                                                           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh......hhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eee....eee.......hhhhhhhhhhhhhhh..eeeeee............hhhhh........hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh.....eeeee..eee..................eee.hhhhhhhhhhhh..--------------..hhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh...eeeeee........eeeeeee.......eeeeehhhhhhhhhhhh...---------......eeeeeeeeehhhhhhhhhhhh.....ee.................ee.hhhhhhhhh......eeeee.hhhhh.....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...........eee....eee....eeeehhhhhh..hhhhhhhhh.hhh.eee....eeeee..eee..eeee.eeeee.........eee..eeee....eeee............hhhhhh..eeee....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oh4 A   3 NPSNSNLQALREELCTPGLDQGHLFEGWPETVDECNERQIALLTDLYMFSNMYPGGVAQYIRNGHELLARESEEVDFAALEMPPLIFEAPSLHRRTAERTALENAGTAMLCKTVFVLVAGGLGERLGYSSIKVSLPVETATNTTYLAYYLRWAQRVGGKEVPFVIMTSDDTHDRTLQLLRELQLEVPNLHVLKQGQVFCFADSAAHLALDETGKLLRKPHGHGDVHSLIYNATV--------------AQPLVNDWLAAGYESIVFIQDTNAGATITIPISLALSAEHSLDMNFTCIPRVPKEPIGLLCRTKKNSGDPWLVANVEYNVFAEVSRALNKD---------GFSPFPGSVNTLVFKLSSYVDRLRESHGIVPEFINPKYSDETRRSFKKPARIESLMQDIALLFSEDDYRVGGTVFERFSYQPVKNSLEEAAGLVAQGNGAYCAATGEAAFYELQRRRLKAIGLPLFYSSQPEVTVAKDAFGVRLFPIIVLDTVCASSGSLDDLARVFPTPEKVHIDQHSTLIVEGRVIIESLELYGALTIRGPTDSMALPHVVRNAVVRNAGWSVHAILSLCAGRDSRLSEVDRIRGFVLKKTAMAVMDC 610
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   |     -       252       262       272       282       292       302       312       322       332        |-       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602        
                                                                                                                                                                                                                                                                   236            251                                                                                       341       351
   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 3OH4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OH4)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D3G6S4_LEIMA | D3G6S4)
molecular function
    GO:0070569    uridylyltransferase activity    Catalysis of the transfer of an uridylyl group to an 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UPG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:495 - Pro A:496   [ 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
  3oh4
    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
  D3G6S4_LEIMA | D3G6S4
    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)
  2.7.7.64
    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
  D3G6S4_LEIMA | D3G6S4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D3G6S4_LEIMA | D3G6S4: 3ogz 3oh0 3oh1 3oh2 3oh3

(-) Related Entries Specified in the PDB File

3ogz 3oh0 3oh1 3oh2 3oh3