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

(-) Description

Title :  STRUCTURE OF CDP-D-GLUCOSE 4,6-DEHYDRATASE FROM SALMONELLA TYPHI
 
Authors :  N. M. Koropatkin, H. M. Holden
Date :  15 Dec 04  (Deposition) - 26 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Short-Chain Dehydrogenase/Reductase, Rossmann Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Koropatkin, H. M. Holden
Structure Of Cdp-D-Glucose 4, 6-Dehydratase From Salmonella Typhi Complexed With Cdp-D-Xylose.
Acta Crystallogr. , Sect. D V. 61 365 2005
PubMed-ID: 15805590  |  Reference-DOI: 10.1107/S0907444904033876

(-) Compounds

Molecule 1 - CDP-GLUCOSE 4,6-DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDHB
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI
    Organism Taxid: 220341
    Strain: CT18

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
2CXY1Ligand/IonCYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1APR4Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
2CXY2Ligand/IonCYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:18 , THR A:20 , GLY A:21 , PHE A:22 , LYS A:23 , ALA A:42 , LEU A:43 , GLY A:66 , ASP A:67 , ILE A:68 , ARG A:69 , MET A:89 , ALA A:90 , ALA A:91 , PRO A:93 , LYS A:104 , THR A:108 , ILE A:132 , TYR A:159 , LYS A:163 , ARG A:208 , HOH A:1602 , HOH A:1603 , HOH A:1606 , HOH A:1607 , HOH A:1612 , HOH A:1618 , HOH A:2533 , HOH A:2535BINDING SITE FOR RESIDUE APR A 400
2AC2SOFTWAREPRO A:93 , VAL A:95 , SER A:134 , ASP A:135 , LYS A:136 , TYR A:159 , ASN A:197 , ASP A:207 , ARG A:208 , LEU A:209 , ASP A:212 , ILE A:224 , ILE A:225 , ARG A:226 , ASN A:227 , SER A:230 , ARG A:232 , VAL A:274 , GLU A:301 , HOH A:1655 , HOH A:1729 , HOH A:1730 , HOH A:1806 , HOH A:1807 , HOH A:2536 , HOH A:2709BINDING SITE FOR RESIDUE CXY A 401
3AC3SOFTWAREGLY B:1018 , HIS B:1019 , THR B:1020 , GLY B:1021 , PHE B:1022 , LYS B:1023 , ALA B:1042 , LEU B:1043 , PRO B:1046 , GLY B:1066 , ASP B:1067 , ILE B:1068 , ARG B:1069 , MET B:1089 , ALA B:1090 , ALA B:1091 , PRO B:1093 , ILE B:1132 , THR B:1133 , TYR B:1159 , LYS B:1163 , HOH B:1791BINDING SITE FOR RESIDUE APR B 1400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:48 -Pro A:49
2Val B:1048 -Pro B:1049

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WVG)

(-) 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:352
 aligned with RFBG_SALTY | P26397 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:356
                                    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       350      
          RFBG_SALTY      1 MIDKNFWQGKRVFVTGHTGFKGSWLSLWLTEMGAIVKGYALDAPTVPSLFEIVRLNDLMESHIGDIRDFEKLRNSIAEFKPEIVFHMAAQPLVRLSYEQPIETYSTNVMGTVHLLETVKQVGNIKAVVNITSDKCYDNREWVWGYRENEPMGGYDPYSNSKGCAELVASAFRNSFFNPANYEQHGVGLASVRAGNVIGGGDWAKDRLIPDILRSFENNQQVIIRNPYSIRPWQHVLEPLSGYIVVAQRLYTEGAKFSEGWNFGPRDEDAKTVEFIVDKMVTLWGDDASWLLDGENHPHEAHYLKLDCSKANMQLGWHPRWGLTETLGRIVKWHKAWIRGEDMLICSKREISDYMSA  356
               SCOP domains -d1wvga1 A:4-358 CDP-glucose-4,6-dehydratase                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1wvgA01 A:3-195 NAD(P)-binding Rossmann-like Domain                                                                                                                                              1wvgA02 A:196-358 UDP-galactose 4-epimerase, domain 1                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh.eeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee........hhhhhhhhhhhh...eee........eeehhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhh.hhhhhhhhhhhhhh....eee.----..........hhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wvg A    3 SIDKNFWQGKRVFVTGHTGFKGSWLSLWLTEMGAIVKGYALDAPTVPSLFEIVRLNDLMESHIGDIRDFEKLRSSIAEFKPEIVFHMAAQPLVRLSYEQPIKTYSTNVMGTVHLLETVKQVGNIKAVVNITSDKCYDNREWVWGYRENEPMGGYDPYSNSKGCAELVASAFRNSFFNPANYEQHGVGLASVRAGNVIGGGDWAKDRLIPDILRSFENNQQVIIRNPYSIRPWQHVLEPLSGYIVVAQRLYTEGAKFSEGWNFGPRDEDAKTVEFIVDKMVTLWGDDASWLLD----PHEAHYLKLDCSKANMQLGWHPRWGLTETLSRIVKWHKAWIRGEDMLICSKREISDYMSA  358
                                    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      
                                                                                                                                                                                                                                                                                                                             294  299                                                           


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with RFBG_SALTY | P26397 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:355
                                    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       350     
          RFBG_SALTY      1 MIDKNFWQGKRVFVTGHTGFKGSWLSLWLTEMGAIVKGYALDAPTVPSLFEIVRLNDLMESHIGDIRDFEKLRNSIAEFKPEIVFHMAAQPLVRLSYEQPIETYSTNVMGTVHLLETVKQVGNIKAVVNITSDKCYDNREWVWGYRENEPMGGYDPYSNSKGCAELVASAFRNSFFNPANYEQHGVGLASVRAGNVIGGGDWAKDRLIPDILRSFENNQQVIIRNPYSIRPWQHVLEPLSGYIVVAQRLYTEGAKFSEGWNFGPRDEDAKTVEFIVDKMVTLWGDDASWLLDGENHPHEAHYLKLDCSKANMQLGWHPRWGLTETLGRIVKWHKAWIRGEDMLICSKREISDYMS  355
               SCOP domains d1wvgb_ B: CDP-glucose-4,6-dehydratase                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1wvgB01 B:1003-1195 NAD(P)-binding Rossmann-like Domain                                                                                                                                          1wvgB02 B:1196-1357 UDP-galactose 4-epimerase, domain 1                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhheeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh.......ee.........hhhhhhhhhhhhhhhhhhhhhh....--....eeeeee...ee........hhhhhhhhhhhh...eee.....ee..eehhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhheehhhhhhhhhhhhh.-..eee.......--...ee.hhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wvg B 1003 SIDKNFWQGKRVFVTGHTGFKGSWLSLWLTEMGAIVKGYALDAPTVPSLFEIVRLNDLMESHIGDIRDFEKLRSSIAEFKPEIVFHMAAQPLVRLSYEQPIKTYSTNVMGTVHLLETVKQVGNIKAVVNITSDKCYDNREWVWGYRENEPMGGYDPYSNSKGCAELVASAFRNSFFNPAN--QHGVGLASVRAGNVIGGGDWAKDRLIPDILRSFENNQQVIIRNPYSIRPWQHVLEPLSGYIVVAQRLYTEGAKFSEGWNFGPRDEDAKTVEFIVDKMVTLWGD-ASWLLDGENHPH--HYLKLDCSKANMQLGWHPRWGLTETLSRIVKWHKAWIRGEDMLICSKREISDYMS 1357
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182  |   1192      1202      1212      1222      1232      1242      1252      1262      1272      1282    | 1292       | -|     1312      1322      1332      1342      1352     
                                                                                                                                                                                                            1182  |                                                                                                  1287 |       1300  |                                                      
                                                                                                                                                                                                               1185                                                                                                    1289          1303
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WVG)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RFBG_SALTY | P26397)
molecular function
    GO:0047733    CDP-glucose 4,6-dehydratase activity    Catalysis of the reaction: CDP-D-glucose = CDP-4-dehydro-6-deoxy-D-glucose + H(2)O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    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.

 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
    APR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CXY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:48 - Pro A:49   [ RasMol ]  
    Val B:1048 - Pro B:1049   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  1wvg
    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
  RFBG_SALTY | P26397
    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)
  4.2.1.45
    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
  RFBG_SALTY | P26397
    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 1WVG)

(-) Related Entries Specified in the PDB File

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