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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENDO-NEURAMINIDASENF MUTANT
 
Authors :  E. C. Schulz, A. Dickmanns, R. Ficner
Date :  31 Mar 09  (Deposition) - 02 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Endo-Neuraminidase; Polysialic Acid; Triple-Beta Helix, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. C. Schulz, D. Schwarzer, M. Frank, K. Stummeyer, M. Muhlenhoff, A. Dickmanns, R. Gerardy-Schahn, R. Ficner
Structural Basis For The Recognition And Cleavage Of Polysialic Acid By The Bacteriophage K1F Tailspike Protein Endonf.
J. Mol. Biol. V. 397 341 2010
PubMed-ID: 20096705  |  Reference-DOI: 10.1016/J.JMB.2010.01.028

(-) Compounds

Molecule 1 - ENDO-N-ACETYLNEURAMINIDASE
    Chains: A
    EC Number: 3.2.1.129
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 246-910
    Gene: SIA, 17, 17.0
    Mutation: YES
    Organism Common: BACTERIOPHAGE K1F
    Organism Scientific: ENTEROBACTERIA PHAGE K1F
    Organism Taxid: 344021
    Synonym: ENDO-ALPHA-SIALIDASE, GP17 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1SIA7Ligand/IonO-SIALIC ACID
2SLB2Ligand/Ion5-N-ACETYL-BETA-D-NEURAMINIC ACID
Biological Unit 1 (2, 27)
No.NameCountTypeFull Name
1SIA21Ligand/IonO-SIALIC ACID
2SLB6Ligand/Ion5-N-ACETYL-BETA-D-NEURAMINIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:1267 , SIA A:2002BINDING SITE FOR RESIDUE SLB A 2001
2AC2SOFTWAREHOH A:162 , SER A:462 , VAL A:464 , THR A:465 , GLY A:466 , VAL A:467 , SER A:468 , HOH A:1091 , HOH A:1166 , HOH A:1267 , HOH A:1324 , SLB A:2001 , SIA A:2003BINDING SITE FOR RESIDUE SIA A 2002
3AC3SOFTWAREHOH A:34 , HOH A:150 , HOH A:218 , PHE A:459 , SER A:460 , ASN A:461 , SER A:468 , THR A:728 , HOH A:1148 , HOH A:1188 , HOH A:1205 , HOH A:1215 , SIA A:2002 , SIA A:2004BINDING SITE FOR RESIDUE SIA A 2003
4AC4SOFTWAREHOH A:174 , ASN A:461 , HOH A:1043 , HOH A:1217 , HOH A:1281 , SIA A:2003 , SIA A:2005BINDING SITE FOR RESIDUE SIA A 2004
5AC5SOFTWAREASN A:461 , LYS A:499 , ASN A:500 , HIS A:502 , HOH A:1217 , HOH A:1428 , SIA A:2004BINDING SITE FOR RESIDUE SIA A 2005
6AC6SOFTWAREHOH A:16 , SER A:808 , ILE A:811 , ARG A:812 , TYR A:821 , THR A:846 , HOH A:1000 , HOH A:1018 , HOH A:1500 , SIA A:2007BINDING SITE FOR RESIDUE SIA A 2006
7AC7SOFTWAREHOH A:16 , HOH A:69 , THR A:846 , SER A:847 , HOH A:1189 , HOH A:1316 , HOH A:1323 , SIA A:2006 , SIA A:2008BINDING SITE FOR RESIDUE SIA A 2007
8AC8SOFTWAREHOH A:105 , HOH A:134 , TYR A:821 , ARG A:837 , THR A:846 , SER A:848 , GLN A:853 , HOH A:1064 , HOH A:1111 , HOH A:1189 , HOH A:1430 , SIA A:2007 , SLB A:2009BINDING SITE FOR RESIDUE SIA A 2008
9AC9SOFTWAREHOH A:79 , HOH A:207 , SER A:848 , ASN A:870 , GLN A:877 , SER A:878 , HOH A:1149 , HOH A:1194 , HOH A:1224 , HOH A:1318 , SIA A:2008BINDING SITE FOR RESIDUE SLB A 2009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GVJ)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:382 -Pro A:383
2Met A:503 -Gly A:504
3Ala A:547 -Pro A:548

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GVJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GVJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3GVJ)

(-) 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:670
 aligned with FIBER_BPK1F | Q04830 from UniProtKB/Swiss-Prot  Length:1064

    Alignment length:722
                                   198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908  
          FIBER_BPK1F   189 VPAGSTPETSGGIGLGAWVSVGDAALRSQISNPEGAILYPELHRARWLDEKDARGWGAKGDGVTDDTAALTSALNDTPVGQKINGNGKTYKVTSLPDISRFINTRFVYERIPGQPLYYASEEFVQGELFKITDTPYYNAWPQDKAFVYENVIYAPYMGSDRHGVSRLHVSWVKSGDDGQTWSTPEWLTDLHPDYPTVNYHCMSMGVCRNRLFAMIETRTLAKNALTNCALWDRPMSRSLHLTGGITKAANQRYATIHVPDHGLFVGDFVNFSNSAVTGVSGDMTVATVIDKDNFTVLTPNQQTSDLNNAGKNWHMGTSFHKSPWRKTDLGLIPSVTEVHSFATIDNNGFAMGYHQGDVAPREVGLFYFPDAFNSPSNYVRRQIPSEYEPDASEPCIKYYDGVLYLITRGTRGDRLGSSLHRSRDIGQTWESLRFPHNVHHTTLPFAKVGDDLIMFGSERAENEWEAGAPDDRYKASYPRTFYARLNVNNWNADDIEWVNITDQIYQGGIVNSGVGVGSVVVKDNYIYYMFGGEDHFNPWTYGDNSAKDPFKSDGHPSDLYCYKMKIGPDNRVSRDFRYGAVPNRAVPVFFDTNGVRTVPAPMEFTGDLGLGHVTIRASTSSNIRSEVLMEGEYGFIGKSIPTDNPAGQRIIFCGGEGTSSTTGAQITLYGANNTDSRRIVYNGDEHLFQSADVKPYNDNVTALGGPSNRFTTAYLGSNPIVT 910
               SCOP domains d3gvj                                                    a1 A:241-760 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     d3gvja2 A:761-910 automated matches                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....----------------------------------------------------...eeeeehhhhhhhhhhhh.....ee....eee.....hhh.ee..eeee.......eeee......eeeee......eee......eee..eeeeeeeee........eeeeeee..........ee..........eeee...eeee..eeeeeeeeee.....eeeeeeeeee...eeeee..eee.....eeeee..........eeeee........eeee..eeee..eeeee........ee....eeeeee.......eeeeee......eeeeeee.....eeeeeee......eeeeeee..........eeee.hhhhh..eeeeeeeee..eeeeeeee........eeeee.......eeee...........eeee..eeeeeee.....................eeeeeeee...........eeeee............eeeeeeee..eeeeeeee.........................eeeeeeee.......................ee.....ee..............................................hhhh.eeeee.....hhhhh.eeeee.........eeee........................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gvj A 241 VPRGS----------------------------------------------------AKGDGVTDDTAALTSALNDTPVGQKINGNGKTYKVTSLPDISRFINTRFVYERIPGQPLYYASEEFVQGELFKITDTPYYNAWPQDKAFVYENVIYAPYMGSDRHGVSRLHVSWVKSGDDGQTWSTPEWLTDLHPDYPTVNYHCMSMGVCRNRLFAMIETRTLAKNALTNCALWDRPMSRSLHLTGGITKAANQRYATIHVPDHGLFVGDFVNFSNSAVTGVSGDMTVATVIDKDNFTVLTPNQQTSDLNNAGKNWHMGTSFHKSPWRKTDLGLIPSVTEVHSFATIDNNGFAMGYHQGDVAPREVGLFYFPDAFNSPSNYVRRQIPSEYEPDASEPCIKYYDGVLYLITRGTRGDRLGSSLHRSRDIGQTWESLRFPHNVHHTTLPFAKVGDDLIMFGSEAAENEWEAGAPDDRYKASYPRTFYARLNVNNWNADDIEWVNITDQIYQGGIVNSGVGVGSVVVKDNYIYYMFGGEDHFNPWTYGDNSAKDPFKSDGHPSDLYCYKMKIGPDNRVSRDFRYGAVPNRAVPVFFDTNGVRTVPAPMEFTGDLGLGHVTIRASTSSNIRSEVLMEGEYGFIGKSIPTDNPAGQRIIFCGGEGTSSTTGAQITLYGANNTDSRRIVYNGDEHLFQSADVKPYNDNVTALGGPSNRFTTAYLGSNPIVT 910
                                |    -         -         -         -         -       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908  
                              245                                                  246
   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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GVJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GVJ)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (FIBER_BPK1F | Q04830)
molecular function
    GO:0016996    endo-alpha-(2,8)-sialidase activity    Catalysis of the endohydrolysis of (2->8)-alpha-sialosyl linkages in oligo- or poly(sialic) acids.
    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.
biological process
    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.

 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
    SIA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SLB  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:547 - Pro A:548   [ RasMol ]  
    Met A:503 - Gly A:504   [ RasMol ]  
    Tyr A:382 - Pro A:383   [ 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
  3gvj
    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
  FIBER_BPK1F | Q04830
    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)
  3.2.1.129
    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
  FIBER_BPK1F | Q04830
    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
        FIBER_BPK1F | Q04830: 1v0e 1v0f 3gvk 3gvl 3gw6 3ju4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GVJ)