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 :  CPGH89CBM32-6 PRODUCED BY CLOSTRIDIUM PERFRINGENS
 
Authors :  E. Ficko-Blean, C. P. Stuart, M. D. Suits, M. Cid, M. Tessier, R. J. Woods A. B. Boraston
Date :  06 Oct 11  (Deposition) - 04 Apr 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Family 89 Glycoside Hydrolase, Family 32 Carbohydrate- Binding Module, Cpf_0859 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ficko-Blean, C. P. Stuart, M. D. Suits, M. Cid, M. Tessier, R. J. Woods, A. B. Boraston
Carbohydrate Recognition By An Architecturally Complex Alpha-N-Acetylglucosaminidase From Clostridium Perfringens.
Plos One V. 7 33524 2012
PubMed-ID: 22479408  |  Reference-DOI: 10.1371/JOURNAL.PONE.0033524

(-) Compounds

Molecule 1 - ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN
    Chains: A, B
    EC Number: 3.2.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: CBM32-4, RESIDUES 1496-1621
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502
    Synonym: GH89_CBM32-4

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:1517 , ASP A:1520 , ASN A:1522 , THR A:1525 , GLY A:1614 , GLU A:1615BINDING SITE FOR RESIDUE CA A1690
2AC2SOFTWAREASN B:1517 , ASP B:1520 , ASN B:1522 , THR B:1525 , GLY B:1614 , GLU B:1615BINDING SITE FOR RESIDUE CA B1690

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A42)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A42)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A42)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A42)

(-) Exons   (0, 0)

(no "Exon" information available for 4A42)

(-) 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:127
 aligned with Q8XM24_CLOPE | Q8XM24 from UniProtKB/TrEMBL  Length:2104

    Alignment length:127
                                  1513      1523      1533      1543      1553      1563      1573      1583      1593      1603      1613      1623       
        Q8XM24_CLOPE   1504 PENLAMKDETKVEVTSNNSEANNLRDGNENTLWIPEQEEEKSVTFDLSKEKDISAIDIVSKGNSPLKYSIEISNDGTEWTKIVDENNNEENKAVYSNILKSGKIGRFVRFNFNSENVKIGEIKIYKG 1630
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhh...eeee..hhhhhhhhhh..............eeeeeeeeeeee..eeeeee.......eeeeee......eeeeee........eeeee.....eeeeeeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a42 A 1495 SENLAmKDETKVEVTSNNSEANNLRDGNENTLWVPGQEEEKSVTFDLSKEKDISAIDIVSKGNSPLKYSIEISNDGTEWTKIVDENNNEENKAVYSNILKSGKIGRFVRFNFNSENVKIGEIKIYKG 1621
                                 |1504      1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614       
                                 |                                                                                                                         
                              1500-MSE                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with Q8XM24_CLOPE | Q8XM24 from UniProtKB/TrEMBL  Length:2104

    Alignment length:126
                                  1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614      1624      
        Q8XM24_CLOPE   1505 ENLAMKDETKVEVTSNNSEANNLRDGNENTLWIPEQEEEKSVTFDLSKEKDISAIDIVSKGNSPLKYSIEISNDGTEWTKIVDENNNEENKAVYSNILKSGKIGRFVRFNFNSENVKIGEIKIYKG 1630
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhh...eeee..hhhhhhhhhh..............eeeeeeeeeeeeeeeeeeee.......eeeeee.....eeeeeee........eeeeeeeeeeeeeeeeeee......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                4a42 B 1496 ENLAmKDETKVEVTSNNSEANNLRDGNENTLWVPGQEEEKSVTFDLSKEKDISAIDIVSKGNSPLKYSIEISNDGTEWTKIVDENNNEENKAVYSNILKSGKIGRFVRFNFNSENVKIGEIKIYKG 1621
                                | 1505      1515      1525      1535      1545      1555      1565      1575      1585      1595      1605      1615      
                             1500-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  (0, 0)

(no "SCOP Domain" information available for 4A42)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A42)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A42)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8XM24_CLOPE | Q8XM24)
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 ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4a42)
 
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
  4a42
    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
  Q8XM24_CLOPE | Q8XM24
    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)
  3.2.1.50
    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
  Q8XM24_CLOPE | Q8XM24
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8XM24_CLOPE | Q8XM24: 4a41 4a44 4a45 4a4a 4aax

(-) Related Entries Specified in the PDB File

2vc9 FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
2vca FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH BETA-N-ACETYL-D-GLUCOSAMINE
2vcb FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH PUGNAC
2vcc FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS
4a3z CPGH89CBM32-4 (SELENO-METHIONINE LABELED) PRODUCED BY CLOSTRIDIUM PERFRINGENS
4a41 CPGH89CBM32-5, FROM CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH GALACTOSE
4a43 CPGH89CBM32-5, FROM CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH GALNAC
4a44 CPGH89CBM32-5, FROM CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH THE TN ANTIGEN
4a45 CPGH89CBM32-5, FROM CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH GALNAC-BETA-1,3-GALACTOSE
4a4a CPGH89 (E483Q, E601Q), FROM CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH ITS SUBSTRATE GLCNAC-ALPHA-1,4-GALACTOSE