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
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)

(-) Description

Title :  FAMILY 51 CARBOHYDRATE BINDING MODULE FROM A FAMILY 98 GLYCOSIDE HYDROLASE PRODUCED BY CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH BLOOD GROUP B-TRISACCHARIDE LIGAND.
 
Authors :  K. J. Gregg, R. Finn, D. W. Abbott, A. B. Boraston
Date :  05 Feb 08  (Deposition) - 19 Feb 08  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Family 51 Carbohydrate Binding Module, Clostridium Perfringens, Family 98 Glycoside Hydrolase, B-Trisaccharide, Blood Group Antigens, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Gregg, R. Finn, D. W. Abbott, A. B. Boraston
Divergent Modes Of Glycan Recognition By A New Family Of Carbohydrate-Binding Modules
J. Biol. Chem. V. 283 12604 2008
PubMed-ID: 18292090  |  Reference-DOI: 10.1074/JBC.M709865200

(-) Compounds

Molecule 1 - CPE0329
    Atcc: 13124
    Chains: A, B
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 DE3 STAR
    Expression System Taxid: 469008
    Fragment: CARBOHYDRATE-BINDING MODULE FAMILY 51, RESIDUES 27-206
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: GLYCOSIDE HYDROLASE FAMILY 98

 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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL4Ligand/IonBETA-D-GALACTOSE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:70 , THR B:191 , TRP B:192 , GLY B:193 , GLU B:195 , GAL B:1212 , FUC B:1213 , HOH B:2284 , HOH B:2285 , HOH B:2286BINDING SITE FOR RESIDUE GAL B1211
2AC2SOFTWARETYR B:135 , GLU B:176 , LYS B:206 , GAL B:1211 , FUC B:1213 , HOH B:2272 , HOH B:2273 , HOH B:2287BINDING SITE FOR RESIDUE GAL B1212
3AC3SOFTWAREASP B:56 , THR B:58 , LYS B:61 , GAL B:1211 , GAL B:1212 , HOH B:2285BINDING SITE FOR RESIDUE FUC B1213
4AC4SOFTWARETHR A:70 , ILE A:99 , THR A:191 , TRP A:192 , GLY A:193 , GLU A:195 , GAL A:1211 , FUC A:1212 , HOH A:2280 , HOH A:2281 , HOH A:2282 , HOH A:2283BINDING SITE FOR RESIDUE GAL A1210
5AC5SOFTWARETYR A:135 , TRP A:192 , LYS A:206 , GAL A:1210 , FUC A:1212 , HOH A:2277 , HOH A:2284 , HOH A:2285 , HOH B:2113BINDING SITE FOR RESIDUE GAL A1211
6AC6SOFTWAREASP A:56 , THR A:58 , LYS A:61 , GAL A:1210 , GAL A:1211 , HOH A:2055 , HOH A:2282BINDING SITE FOR RESIDUE FUC A1212
7AC7SOFTWARELYS A:137 , ALA A:187 , LYS A:190 , ASP A:194 , HOH A:2181 , HOH A:2264BINDING SITE FOR RESIDUE CA A1213
8AC8SOFTWARELYS B:137 , ALA B:187 , LYS B:190 , ASP B:194 , HOH B:2184 , HOH B:2260BINDING SITE FOR RESIDUE CA B1214

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:102 -Pro A:103
2Ser B:102 -Pro B:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VNO)

(-) 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:171
 aligned with Q8XNK4_CLOPE | Q8XNK4 from UniProtKB/TrEMBL  Length:795

    Alignment length:171
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203 
         Q8XNK4_CLOPE    34 SRDVYLSDLDWLNATHGDDTKSKIVQKNHPFTPGNNNQSTKISLKMEDGSISEFEKGLGTIAGSPSTITYDISGAGVTKFFSYLGIDRSANPINEQYAKVDKIEVVVDGKVIYSTINQFPNGLTYETPAIKVDLNIPENAKRLQLKSYAGEKTWGDEVVYADAKFTAKGDF 204
               SCOP domains d2vnoa_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhh...ee...........ee..hhhhhhh.....eeee.....eeee..eee......eeeeee.....eeeeeeeeee............ee.eeeeee..eeeee........ee.....eeeeee......eeeeeee.........eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vno A  39 SRDVYLSDLDWLNATHGDDTKSKIVQKNHPFTPGNNNQSTKISLKMEDGSISEFEKGLGTIAGSPSTITYDISGAGVTKFFSYLGIDRSANPINEQYAKVDKIEVVVDGKVIYSTINQFPNGLTYETPAIKVDLNIPENAKRLQLKSYAGEKTWGDEVVYADAKFTAKGDF 209
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208 


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q8XNK4_CLOPE | Q8XNK4 from UniProtKB/TrEMBL  Length:795

    Alignment length:173
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
         Q8XNK4_CLOPE    33 ESRDVYLSDLDWLNATHGDDTKSKIVQKNHPFTPGNNNQSTKISLKMEDGSISEFEKGLGTIAGSPSTITYDISGAGVTKFFSYLGIDRSANPINEQYAKVDKIEVVVDGKVIYSTINQFPNGLTYETPAIKVDLNIPENAKRLQLKSYAGEKTWGDEVVYADAKFTAKGDFV 205
               SCOP domains d2vnob_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NPCBM-2vnoB01 B:38-205                                                                                                                                                  ----- Pfam domains (1)
           Pfam domains (2) NPCBM-2vnoB02 B:38-205                                                                                                                                                  ----- Pfam domains (2)
         Sec.struct. author ..eeee.hhh...ee...........ee..hhhhhhh.....eeee.....eeee..eeeee....eeeeee.....eeeeeeeeee............ee.eeeeee..eeeee........ee.....eeeeee......eeeeeee........eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vno B  38 ESRDVYLSDLDWLNATHGDDTKSKIVQKNHPFTPGNNNQSTKISLKMEDGSISEFEKGLGTIAGSPSTITYDISGAGVTKFFSYLGIDRSANPINEQYAKVDKIEVVVDGKVIYSTINQFPNGLTYETPAIKVDLNIPENAKRLQLKSYAGEKTWGDEVVYADAKFTAKGDFV 210
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: NPCBM] (4)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8XNK4_CLOPE | Q8XNK4)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GAL  [ 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 ]
 
  Cis Peptide Bonds
    Ser A:102 - Pro A:103   [ RasMol ]  
    Ser B:102 - Pro B:103   [ RasMol ]  
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  2vno
    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
  Q8XNK4_CLOPE | Q8XNK4
    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)
  3.2.1.-
    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
  Q8XNK4_CLOPE | Q8XNK4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8XNK4_CLOPE | Q8XNK4: 2vng 2vnr

(-) Related Entries Specified in the PDB File

2vng FAMILY 51 CARBOHYDRATE BINDING MODULE FROM A FAMILY 98 GLYCOSIDE HYDROLASE PRODUCED BY CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH BLOOD GROUP A-TRISACCHARIDE LIGAND.
2vnr FAMILY 51 CARBOHYDRATE BINDING MODULE FROM A FAMILY 98 GLYCOSIDE HYDROLASE PRODUCED BY CLOSTRIDIUM PERFRINGENS.