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

(-) Description

Title :  STRUCTURE OF E. COLI ADP-HEPTOSE LPS HEPTOSYLTRANSFERASE II
 
Authors :  R. Kniewel, J. Buglino, V. Solorzano, J. Wu, C. D. Lima, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  21 Jun 03  (Deposition) - 08 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, T832, Nysgxrc, Transferase, Lps Biosynthetic Pathway, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Kniewel, J. Buglino, V. Solorzano, J. Wu, C. D. Lima
Structure Of E. Coli Adp-Heptose Lps Heptosyltransferase Ii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADP-HEPTOSE LPS HEPTOSYLTRANSFERASE II
    Chains: A
    EC Number: 2.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET T7
    Expression System Strain: B834 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RFAF
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1PSW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PSW)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:153 -Pro A:154

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PSW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PSW)

(-) Exons   (0, 0)

(no "Exon" information available for 1PSW)

(-) 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:331
 aligned with RFAF_ECOLI | P37692 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:348
                                    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       330       340        
           RFAF_ECOLI     1 MKILVIGPSWVGDMMMSQSLYRTLQARYPQAIIDVMAPAWCRPLLSRMPEVNEAIPMPLGHGALEIGERRKLGHSLREKRYDRAYVLPNSFKSALVPFFAGIPHRTGWRGEMRYGLLNDVRVLDKEAWPLMVERYIALAYDKGIMRTAQDLPQPLLWPQLQVSEGEKSYTCNQFSLSSERPMIGFCPGAEFGPAKRWPHYHYAELAKQLIDEGYQVVLFGSAKDHEAGNEILAALNTEQQAWCRNLAGETQLDQAVILIAACKAIVTNDSGLMHVAAALNRPLVALYGPSSPDFTPPLSHKARVIRLITGYHKVRKGDAAEGYHQSLIDITPQRVLEELNALLLQEEA 348
               SCOP domains d1pswa_ A: ADP-heptose LPS heptosyltransferase II                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -1pswA01 A:2-151 Glycogen Phosphorylase B;                                                                                                             -----------1pswA02 A:163-348 Glycogen Phosphorylase B;                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------       ----Glyco_transf_9-1pswA01 A:69-324                                                                                                                                                                                                                                 ------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhh....eeeeee.-------hhhhhhhhhhhh......eeee....hhhhhhhhhh...eeeee..........eee........hhhhhhhhhhhhhhhh.hhhhh...........hhhhhhhhhhhh.......eeeee.....hhhhh.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhh..hhhhhh.eee.....hhhhhhhhhhh..eeeee.hhhhhhhhhh...eeeee..............eeeee....----------...hhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1psw A   1 mKILVIGPSWVGDmmmSQSLYRTLQARYPQAIIDVmAPAWCRPLLSRmPEVNEAIPm-------EIGERRKLGHSLREKRYDRAYVLPNSFKSALVPLFAGIPHRTGWRGEmRYGLLNDVRVLDKEAWPLmVERYIALAYDKGImRTAQDLPQPLLWPQLQVSEGEKSYTCNQFSLSSERPmIGFCPGAEFGPAKRWPHYHYAELAKQLIDEGYQVVLFGSAKDHEAGNEILAALNTEQQAWCRNLAGETQLDQAVILIAACKAIVTNDSGLmHVAAALNRPLVALYGPSSPDFTPPLSHKARVIRLITG----------EGYHQSLIDITPQRVLEELNALLLQEEA 348
                            |       10   |||  20        30     |  40       |50      |  -    |   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         -|      330       340        
                            |           14-MSE                36-MSE      48-MSE   57-MSE  65                                            112-MSE            131-MSE       145-MSE                              182-MSE                                                                                    273-MSE                              310        321                           
                            1-MSE        15-MSE                                                                                                                                                                                                                                                                                                                                         
                                          16-MSE
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RFAF_ECOLI | P37692)
molecular function
    GO:0008713    ADP-heptose-lipopolysaccharide heptosyltransferase activity    Catalysis of the reaction: heptosyl-KDO2-lipid A + ADP-L-glycero-beta-D-manno-heptose = heptosyl2-KDO2-lipid A + 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:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    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.
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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1psw)
 
  Cis Peptide Bonds
    Gln A:153 - Pro A:154   [ 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
  1psw
    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
  RFAF_ECOLI | P37692
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.4.99.-
    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
  RFAF_ECOLI | P37692
    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 1PSW)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PSW)