Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  ENHANCING THE RECEPTOR AFFINITY OF THE SIALIC ACID-BINDING DOMAIN OF VIBRIO CHOLERAE SIALIDASE THROUGH MULTIVALENCY
 
Authors :  H. Connaris, P. R. Crocker, G. L. Taylor
Date :  17 Dec 08  (Deposition) - 30 Dec 08  (Release) - 10 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cbm, Calcium, Secreted, Hydrolase, Glycosidase, Sialic Acid, Carbohydrate-Binding-Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Connaris, P. R. Crocker, G. L. Taylor
Enhancing The Receptor Affinity Of The Sialic Acid- Binding Domain Of Vibrio Cholerae Sialidase Through Multivalency
J. Biol. Chem. V. 284 7339 2009
PubMed-ID: 19124471  |  Reference-DOI: 10.1074/JBC.M807398200

(-) Compounds

Molecule 1 - SIALIDASE
    Chains: A, B, C
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CBM40 DOMAIN, RESIDUES 25-216
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Synonym: SIALIC ACID BINDING DOMAIN FROM V. CHOLERAESIALIDASE, NANASE, NEURAMINIDASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2CA1Ligand/IonCALCIUM ION
3GAL3Ligand/IonBETA-D-GALACTOSE
4SIA3Ligand/IonO-SIALIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4SIA1Ligand/IonO-SIALIC ACID
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4SIA1Ligand/IonO-SIALIC ACID
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2CA-1Ligand/IonCALCIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:82BINDING SITE FOR RESIDUE CA A1211
02AC2SOFTWAREARG A:74 , ARG A:118 , GLN A:188 , GLY A:196 , SER A:197 , SER A:198 , GAL A:1219 , HOH A:2009 , THR C:139 , GLY C:140BINDING SITE FOR RESIDUE SIA A1217
03AC3SOFTWARESIA A:1217 , BGC A:1220BINDING SITE FOR RESIDUE GAL A1219
04AC4SOFTWAREGAL A:1219BINDING SITE FOR RESIDUE BGC A1220
05AC5SOFTWAREARG B:74 , TYR B:111 , ARG B:118 , GLY B:140 , GLN B:188 , GLY B:196 , SER B:197 , SER B:198 , ASN B:199 , GAL B:1219 , HOH B:2044BINDING SITE FOR RESIDUE SIA B1217
06AC6SOFTWARESER B:198 , SIA B:1217 , BGC B:1220BINDING SITE FOR RESIDUE GAL B1219
07AC7SOFTWAREGAL B:1219BINDING SITE FOR RESIDUE BGC B1220
08AC8SOFTWAREGLY A:140 , ARG C:74 , ARG C:118 , GLN C:188 , GLY C:196 , SER C:197 , SER C:198 , GAL C:1219 , HOH C:2048 , HOH C:2049BINDING SITE FOR RESIDUE SIA C1216
09AC9SOFTWARESIA C:1216 , BGC C:1220BINDING SITE FOR RESIDUE GAL C1219
10BC1SOFTWAREARG A:141 , GAL C:1219BINDING SITE FOR RESIDUE BGC C1220

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W68)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:22 -Ala A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W68)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W68)

(-) Exons   (0, 0)

(no "Exon" information available for 2W68)

(-) 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:195
 aligned with NANH_VIBCH | P0C6E9 from UniProtKB/Swiss-Prot  Length:781

    Alignment length:195
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           NANH_VIBCH    22 SNAALFDYNATGDTEFDSPAKQGWMQDNTNNGSGVLTNADGMPAWLVQGIGGRAQWTYSLSTNQHAQASSFGWRMTTEMKVLSGGMITNYYANGTQRVLPIISLDSSGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQGD 216
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w68A00 A:22-216  [code=2.60.120.200, no name defined]                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhh.hhhhh.ee......eeeeee....eeeeeee....eeeee..hhhhhhhhhhhheeeeeeeeeeee..ee.eee...eee.eeeee.....eeeee......eeeehhhhhhh.eeeeeeee.....eeeeee..eeeeeee..ee.....eeeee......eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w68 A  22 AAMALFDYNATGDTEFDSPAKQGWMQDNTNNGSGVLTNADGMPAWLVQGIGGRAQWTYSLSTNQHAQASSFGWRMTTEMKVLSGGMITNYYANGTQRVLPIISLDSSGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQGD 216
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with NANH_VIBCH | P0C6E9 from UniProtKB/Swiss-Prot  Length:781

    Alignment length:193
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   
           NANH_VIBCH    24 AALFDYNATGDTEFDSPAKQGWMQDNTNNGSGVLTNADGMPAWLVQGIGGRAQWTYSLSTNQHAQASSFGWRMTTEMKVLSGGMITNYYANGTQRVLPIISLDSSGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQGD 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w68B00 B:24-216  [code=2.60.120.200, no name defined]                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhh.hhhhh.ee......eeeee......eeeeee....eeeee..hhhhhhhhhhhheeeeeeeeeeee..ee.eeeeeeee..eeeee.....eeeee......eeeehhhhhhh.eeeeeeee.....eeeeee..eeeeeee..eeeeeeeeeeee......eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w68 B  24 MALFDYNATGDTEFDSPAKQGWMQDNTNNGSGVLTNADGMPAWLVQGIGGRAQWTYSLSTNQHAQASSFGWRMTTEMKVLSGGMITNYYANGTQRVLPIISLDSSGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQGD 216
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   


Chain C from PDB  Type:PROTEIN  Length:194
 aligned with NANH_VIBCH | P0C6E9 from UniProtKB/Swiss-Prot  Length:781

    Alignment length:194
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211    
           NANH_VIBCH    22 SNAALFDYNATGDTEFDSPAKQGWMQDNTNNGSGVLTNADGMPAWLVQGIGGRAQWTYSLSTNQHAQASSFGWRMTTEMKVLSGGMITNYYANGTQRVLPIISLDSSGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQG 215
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w68C00 C:22-215  [code=2.60.120.200, no name defined]                                                                                                                                             CATH domains
           Pfam domains (1) ------------------------------------------Sial-lect-inser-2w68C01 C:64-215                                                                                                                         Pfam domains (1)
           Pfam domains (2) ------------------------------------------Sial-lect-inser-2w68C02 C:64-215                                                                                                                         Pfam domains (2)
           Pfam domains (3) ------------------------------------------Sial-lect-inser-2w68C03 C:64-215                                                                                                                         Pfam domains (3)
         Sec.struct. author ...eeeeee...hhhhhhhhhhh.ee......eeeeee....eeeeee.....eeeee..hhhhhhhhhhhheeeeeeeeeeee.....eeee..eee.eeeee.....eeeee......eeeehhhhhh.eeeeeeeee.....eeeeee...eeeeee..ee...eeeeeee......eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w68 C  22 AAMALFDYNATGDTEFDSPAKQGWMQDNTNNGSGVLTNADGMPAWLVQGIGGRAQWTYSLSTNQHAQASSFGWRMTTEMKVLSGGMITNYYANGTQRVLPIISLDSSGNLVVEFEGQTGRTVLATGTAATEYHKFELVFLPGSNPSASFYFDGKLIRDNIQPTASKQNMIVWGNGSSNTDGVAAYRDIKFEIQG 215
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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 2W68)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: Sial-lect-inser] (4)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NANH_VIBCH | P0C6E9)
molecular function
    GO:0052794    exo-alpha-(2->3)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052795    exo-alpha-(2->6)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->6)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0052796    exo-alpha-(2->8)-sialidase activity    Catalysis of the hydrolysis of alpha-(2->8)-glycosidic linkages of terminal sialic residues in substrates.
    GO:0004308    exo-alpha-sialidase activity    Catalysis of the hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0033691    sialic acid binding    Interacting selectively and non-covalently with sialic acid, any of a variety of N- or O- substituted derivatives of neuraminic acid, a nine carbon monosaccharide. Sialic acids often occur in polysaccharides, glycoproteins, and glycolipids in animals and bacteria.
biological process
    GO:0006689    ganglioside catabolic process    The chemical reactions and pathways resulting in the breakdown of ganglioside, a ceramide oligosaccharide carrying, in addition to other sugar residues, one or more sialic 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.
    GO:0009313    oligosaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:22 - Ala A:23   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 2 PNG format | Biol. Unit 3 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
  2w68
    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
  NANH_VIBCH | P0C6E9
    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)
  3.2.1.18
    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
  NANH_VIBCH | P0C6E9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NANH_VIBCH | P0C6E9: 1kit 1w0o 1w0p

(-) Related Entries Specified in the PDB File

1kit VIBRIO CHOLERAE NEURAMINIDASE
1w0o VIBRIO CHOLERAE SIALIDASE
1w0p VIBRIO CHOLERAE SIALIDASE WITH ALPHA-2,6- SIALYLLACTOSE