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 THE URIDINE DIPHOSPHATE N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH INHIBITOR
 
Authors :  W. Fang, O. G. Raimi, D. M. F. Vanaalten
Date :  30 May 13  (Deposition) - 17 Jul 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Urbaniak, I. T. Collie, W. Fang, T. Aristotelous, S. Eskilsson, O. G. Raimi, J. Harrison, I. Hopkins Navratolova, J. A. Frearson, D. M. F. Van Aalten, M. A. J. Ferguson
A Novel Allosteric Inhibitor Of The Uridine Diphosphate N- Acetylglucosamine Pyrophosphorylase From Trypanosoma Brucei.
Acs Chem. Biol. V. 8 1981 2013
PubMed-ID: 23834437  |  Reference-DOI: 10.1021/CB400411X

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
    Chains: A
    EC Number: 2.7.7.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1-TBUAP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PGEX-6P-1
    Expression System Vector Type: PLASMID
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
19VU1Ligand/Ion(3S)-3-[2-(1,3-BENZODIOXOL-5-YL)-2-OXIDANYLIDENE-ETHYL]-4-BROMANYL-5-METHYL-3-OXIDANYL-1HINDOL-2-ONE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:510 , LEU A:511 , ARG A:512 , HOH A:2388 , HOH A:2389 , HOH A:2391BINDING SITE FOR RESIDUE SO4 A1538
2AC2SOFTWAREGLY A:44 , VAL A:45 , ASP A:46 , HIS A:49 , PHE A:50 , SER A:207 , VAL A:209 , GLY A:232 , ALA A:236 , ALA A:239 , ALA A:367 , MET A:370 , LYS A:371 , TYR A:376 , HOH A:2056 , HOH A:2065 , HOH A:2315BINDING SITE FOR RESIDUE 9VU A1539
3AC3SOFTWAREHIS A:202 , ARG A:245 , HIS A:263 , HOH A:2238 , HOH A:2239 , HOH A:2409BINDING SITE FOR RESIDUE SO4 A1540

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:411 -Pro A:412

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BQH)

(-) 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:521
 aligned with Q386Q8_TRYB2 | Q386Q8 from UniProtKB/TrEMBL  Length:545

    Alignment length:541
                                1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536 
         Q386Q8_TRYB2     - ----MSDRDVCIQRLTGANQDHILTALEHGSEAERASLTAQITNELAGVDFRHFNDVLRESLEISKNCSTASLAEPPAKDSFFDISSVDRRRGQAKRIKNLEAVGYKAIQKGQIAFLILAGGSGTRLGFDKPKGFFTCDGLQQRKSLFMMHCEKIRRRQEIAESISGSGRKARVQLLVMTSGQNDAETQRFFEENSYFGLEREQVHFFAQSSVPCYDENTGRIIMENRGRICAAPGGNGAVFAALAAPRATKDKDGTLQVKESLLQHLRKLGIAYVQIGNIDNLLANVADPVFIGYAIEEEAHVVVKTCPKRGPDERVGVFVRASGKWGVVEYTEIGDRAKEIDDATGELKFNCANISSNLCSLHFMSLAAERMKSFTQYHAARKKIPTIKGPVMGIKLEAFLFDLFRFVDECDHPPKDSGAFRIMQVDRDDEFGPVKNADGAASDTPADAVRLLLSQHTRWLITALETAAMSDEQESIRGGVDVTEAKEAVAVMRSCSIKAEISPLVSVGGEGLRQHLPRVIHQLLRNPPPVIFIRRDDE 537
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.-----..ee.......ee..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...eehhhheeee.hhh.........hhhhhhhhhhhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhhhhhhh.eeeee...ee..........eee..ee.ee..hhhhhhhhhhhee...----.....eehhhhhhhh...eeeeee.........hhhhhhhhhhhh..eeeeee..........eeeee..eeeeehhhhh--................eeeeeeeeehhhhhhhhhhhh.....eeeeeee......eeeeeee.hhhhhhhhhhhhh........eeeee.hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh---------..hhhhhhhhhhhhhhh..eeee..........hhhhhhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bqh A  -3 PLGSMSDRDVCIQRLTGANQDHILTALEHGSEAERASLTAQITNELAGVDFRHFNDVLRESLEISK-----SLAEPPAKDSFFDISSVDRRRGQAKRIKNLEAVGYKAIQKGQIAFLILAGGSGTRLGFDKPKGFFTCDGLQQRKSLFMMHCEKIRRRQEIAESISGSGRKARVQLLVMTSGQNDAETQRFFEENSYFGLEREQVHFFAQSSVPCYDENTGRIIMENRGRICAAPGGNGAVFAALAAPRATK----TLQVKESLLQHLRKLGIAYVQIGNIDNLLANVADPVFIGYAIEEEAHVVVKTCPKRGPDERVGVFVRASGKWGVVEYTEI--RAKEIDDATGELKFNCANISSNLCSLHFMSLAAERMKSFTQYHAARKKIPTIKGPVMGIKLEAFLFDLFRFVDECDHPPKDSGAFRIMQVDRDDEFGPVKNADGAASDTPADAVRLLLSQHTRWLITALETAAM---------GVDVTEAKEAVAVMRSCSIKAEISPLVSVGGEGLRQHLPRVIHQLLRNPPPVIFIRRDDE 537
                                     6        16        26        36        46        56     |   - |      76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246 |    |256       266       276       286       296       306       316       326     | 336       346       356       366       376       386       396       406       416       426       436       446       456       466 |       - |     486       496       506       516       526       536 
                                                                                            62    68                                                                                                                                                                                 248  253                                                                            332  |                                                                                                                                  468       478                                                           
                                                                                                                                                                                                                                                                                                                                                                            335
   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 4BQH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q386Q8_TRYB2 | Q386Q8)
molecular function
    GO:0003977    UDP-N-acetylglucosamine diphosphorylase activity    Catalysis of the reaction: N-acetyl-alpha-D-glucosamine 1-phosphate + UTP = diphosphate + UDP-N-acetyl-alpha-D-glucosamine.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0070569    uridylyltransferase activity    Catalysis of the transfer of an uridylyl group to an acceptor.
biological process
    GO:0006048    UDP-N-acetylglucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    GO:0006011    UDP-glucose metabolic process    The chemical reactions and pathways involving UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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
    9VU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:411 - Pro A:412   [ 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
  4bqh
    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
  Q386Q8_TRYB2 | Q386Q8
    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)
  2.7.7.23
    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
  Q386Q8_TRYB2 | Q386Q8
    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 4BQH)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4BQH)