Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  E. COLI HEPTOSYLTRANSFERASE WAAC.
 
Authors :  S. Grizot, M. Salem, V. Vongsouthi, L. Durand, F. Moreau, H. Dohi, S. Vincent, S. Escaich, A. Ducruix
Date :  27 Apr 06  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gt-B Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Grizot, M. Salem, V. Vongsouthi, L. Durand, F. Moreau, H. Dohi, S. Vincent, S. Escaich, A. Ducruix
Structure Of The Escherichia Coli Heptosyltransferase Waac: Binary Complexes With Adp And Adp-2-Deoxy-2-Fluoro Heptose.
J. Mol. Biol. V. 363 383 2006
PubMed-ID: 16963083  |  Reference-DOI: 10.1016/J.JMB.2006.07.057
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIPOPOLYSACCHARIDE HEPTOSYLTRANSFERASE-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET-30B
    Organism Scientific: ESCHERICHIA COLI UTI89
    Organism Taxid: 364106
    Strain: RS218

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2GT1)

(-) Sites  (0, 0)

(no "Site" information available for 2GT1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GT1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GT1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GT1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GT1)

(-) Exons   (0, 0)

(no "Exon" information available for 2GT1)

(-) Sequences/Alignments

Asymmetric 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:323
 aligned with Q1R4X0_ECOUT | Q1R4X0 from UniProtKB/TrEMBL  Length:326

    Alignment length:323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   
         Q1R4X0_ECOUT     1 MRVLIVKTSSMGDVLHTLPALTDAQQAIPGIKFDWVVEEGFAQIPSWHAAVERVIPVAIRRWRKAWFSAPIKAERKAFREALQAKNYDAVIDAQGLVKSAALVTRLAHGVKHGMDWQTAREPLASLFYNRKHHIAKQQHAVERTRELFAKSLGYSKPQTQGDYAIAQHFLTNLPTDAGEYAVFLHATTRDDKHWPEEHWRELIGLLADSGIRIKLPWGAPHEEERAKRLAEGFAYVEVLPKMSLEGVARVLAGAKFVVSVDTGLSHLTAALDRPNITVYGPTDPGLIGGYGKNQMVCRAPGNELSQLTANAVKQFIEENAEKA 323
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhh...eeeeeeehhhhhhh...hhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh...eeee......hhhhhhhh.eee......hhhhhhhhhhhhhhh...........hhhhhhh........eeeee....hhhhh.hhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh....eee....hhhhhhhhhhh..eeeee.hhhhhhhhhh...eeeee...hhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gt1 A   1 MRVLIVKTSSMGDVLHTLPALTDAQQAIPGIKFDWVVEEGFAQIPSWHAAVERVIPVAIRRWRKAWFSAPIKAERKAFREALQAKNYDAVIDAQGLVKSAALVTRLAHGVKHGMDWQTAREPLASLFYNRKHHIAKQQHAVERTRELFAKSLGYSKPQTQGDYAIAQHFLTNLPTDAGEYAVFLHATTRDDKHWPEEHWRELIGLLADSGIRIKLPWGAPHEEERAKRLAEGFAYVEVLPKMSLEGVARVLAGAKFVVSVDTGLSHLTAALDRPNITVYGPTDPGLIGGYGKNQMVCRAPGNELSQLTANAVKQFIEENAEKA 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with Q1R4X0_ECOUT | Q1R4X0 from UniProtKB/TrEMBL  Length:326

    Alignment length:326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
         Q1R4X0_ECOUT     1 MRVLIVKTSSMGDVLHTLPALTDAQQAIPGIKFDWVVEEGFAQIPSWHAAVERVIPVAIRRWRKAWFSAPIKAERKAFREALQAKNYDAVIDAQGLVKSAALVTRLAHGVKHGMDWQTAREPLASLFYNRKHHIAKQQHAVERTRELFAKSLGYSKPQTQGDYAIAQHFLTNLPTDAGEYAVFLHATTRDDKHWPEEHWRELIGLLADSGIRIKLPWGAPHEEERAKRLAEGFAYVEVLPKMSLEGVARVLAGAKFVVSVDTGLSHLTAALDRPNITVYGPTDPGLIGGYGKNQMVCRAPGNELSQLTANAVKQFIEENAEKAAMI 326
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhh...eeeeeee.hhh.hhhhh..eeeeeeehhhhhh.----------hhhhhhhhh.....eeee...hhhhhhhh.......eeee......hhhhhhhh.eee......hhhhhhhhhhhhhhh...........hhhhhhh.-----...eeee....hhhhh.hhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhh....eee....hhhhhhhhhhhh.eeeee.hhhhhhhhhh...eeeee.....--------..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gt1 B   1 MRVLIVKTSSMGDVLHTLPALTDAQQAIPGIKFDWVVEEGFAQIPSWHAAVERVIPVAIRRWRK----------RKAFREALQAKNYDAVIDAQGLVKSAALVTRLAHGVKHGMDWQTAREPLASLFYNRKHHIAKQQHAVERTRELFAKSLGYSKPQTQGDYAIAQHFLTN-----GEYAVFLHATTRDDKHWPEEHWRELIGLLADSGIRIKLPWGAPHEEERAKRLAEGFAYVEVLPKMSLEGVARVLAGAKFVVSVDTGLSHLTAALDRPNITVYGPTDP--------NQMVCRAPGNELSQLTANAVKQFIEENAEKAAMI 326
                                    10        20        30        40        50        60   |     -    |   80        90       100       110       120       130       140       150       160       170 |     180       190       200       210       220       230       240       250       260       270       280   |     -  |    300       310       320      
                                                                                          64         75                                                                                              172   178                                                                                                       284      293
   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 2GT1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GT1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GT1)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q1R4X0_ECOUT | Q1R4X0)
molecular function
    GO:0008920    lipopolysaccharide heptosyltransferase activity    Catalysis of the reaction: a lipopolysaccharide + ADP-L-glycero-beta-D-manno-heptose = a heptosylated lipopolysaccharide + ADP + H+.
    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).
biological process
    GO:0009244    lipopolysaccharide core region biosynthetic process    The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
    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 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 2gt1)
 
  Sites
(no "Sites" information available for 2gt1)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gt1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  2gt1
    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
  Q1R4X0_ECOUT | Q1R4X0
    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
  Q1R4X0_ECOUT | Q1R4X0
    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 2GT1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GT1)