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 PUTATIVE UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE FROM ENTAMOEBA HISTOLYTICA
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Aug 10  (Deposition) - 18 Aug 10  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Anaerobic Parasitic Protozoan, Amoebic Dysentery, Amoebic Liver Abscess, Cysts, Udp-N-Acetylglucosamine Diphosphorylase, Transferase, Nucleotidyl Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, A. S. Gardberg, I. Q. Phan, Y. Zhang, B. L. Staker, P. J. Myler, D. D. Lorimer
Structure Of Uridine Diphosphate N-Acetylglucosamine Pyrophosphorylase From Entamoeba Histolytica.
Acta Crystallogr F Struct V. 71 560 2015 Biol Commun
PubMed-ID: 25945709  |  Reference-DOI: 10.1107/S2053230X1500179X

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
    Chains: A
    EC Number: 2.7.7.23
    Engineered: YES
    Gene: EHI_021200
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 294381

 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
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:22 , GLN A:29 , LYS A:31BINDING SITE FOR RESIDUE SO4 A 402
2AC2SOFTWAREGLN A:126 , PRO A:150 , GLY A:152 , HIS A:153 , HOH A:504 , HOH A:561 , HOH A:724BINDING SITE FOR RESIDUE EDO A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OC9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:396 -Pro A:397

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OC9)

(-) Exons   (0, 0)

(no "Exon" information available for 3OC9)

(-) 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:400
 aligned with C4M036_ENTHI | C4M036 from UniProtKB/TrEMBL  Length:401

    Alignment length:400
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401
         C4M036_ENTHI     2 TYQPVDITTNTIPVTKEHYYRGLELISQGKTALITLAGGQGSRLGFEHPKGMFVLPFEIPKSIFQMTSERLLRLQELASEYSHQKNVMIHWFLMTNEETIEEINNYFKEHQYFGLSSEQIHCFPQGMLPVVDFNGKILYEKKDKPYMAPNGHGGLFKALKDNGILEFMNEKGIKYSVAHNVDNILCKDVDPNMIGYMDLLQSEICIKIVKKGFKEEKVGVLVKEQERIKVVEYTELTDELNKQLSNGEFIYNCGHISINGYSTSFLEKAAEYQLPYHIAKKKVPFVNEQGIVIHPSENNGIKKEMFFFDVFPLATKVSIFEIQRFIEFSALKNSLNESFDNVNTVKRDWYRLNIYYLKKAGAIVDDSKSPICEISFRKSFEEEGLKEFKGKTIQLPFILQ 401
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------UDPGP-3oc9A01 A:10-376                                                                                                                                                                                                                                                                                                                                                         ------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhh..eeeeee............hhhh.ee.....eehhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhh....eeeee..eee.........eee..ee.eee.hhhhhhhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhh...eeeeeee.........eeeee..eeeeehhhhh................eeeeeeeeeehhhhhhhh......eeeee...ee.....ee......eeeee.hhhhhhhhh..eeeee.hhhhhh............hhhhhhhhhhhhhhhhhhhh..eee......eee.......hhhhhhhh..eee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oc9 A   2 TYQPVDITTNTIPVTKEHYYRGLELISQGKTALITPAGGQGSRLGFEHPKGMFVLPFEIPKSIFQMTSERLLRLQELASEYSHQKNVMIHWFLMTNEETIEEINNYFKEHQYFGLSSEQIHCFPQGMLPVVDFNGKILYEKKDKPYMAPNGHGGLFKALKDNGILEFMNEKGIKYSVAHNVDNILCKDVDPNMIGYMDLLQSEICIKIVKKGFKEEKVGVLVKEQERIKVVEYTELTDELNKQLSNGEFIYNCGHISINGYSTSFLEKAAEYQLPYHIAKKKVPFVNEQGIVIHPSENNGIKKEIFFFDVFPLATKVSIFEIQRFIEFSALKNSLNESFDNVNTVKRDWYRLNIYYLKKAGAIVDDSKSPICEISFRKSFEEEGLKEFKGKTIQLPFILQ 401
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401
   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 3OC9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OC9)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C4M036_ENTHI | C4M036)
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: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: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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:396 - Pro A:397   [ 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
  3oc9
    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
  C4M036_ENTHI | C4M036
    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
  C4M036_ENTHI | C4M036
    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 3OC9)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3OC9)