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

(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-HEXOSAMINIDASE FROM VIBRIO CHOLERAE IN COMPLEX WITH N-ACETYL-D-GLUCOSAMINE TO A RESOLUTION OF 1.85
 
Authors :  J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Center F Structural Genomics (Nysgxrc)
Date :  03 Dec 04  (Deposition) - 14 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha Barrel, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Gorman, L. Shapiro
Crystal Structure Of Beta-Hexosaminidase From Vibrio Cholerae In Complex With N-Acetyl-D-Glucosamine To A Resolution Of 1. 85
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-HEXOSAMINIDASE
    ChainsA
    EC Number3.2.1.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneNAGZ
    Organism ScientificVIBRIO CHOLERAE
    Organism Taxid666
    SynonymN-ACETYL-BETA-GLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:62 , ARG A:130 , LYS A:160 , HIS A:161 , MET A:204 , GLU A:247 , HOH A:547 , HOH A:766 , HOH A:884BINDING SITE FOR RESIDUE NAG A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y65)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:115 -Pro A:116
2Lys A:160 -His A:161
3Phe A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y65)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F3PS00775 Glycosyl hydrolases family 3 active site.NAGZ_VIBCH228-245  1A:228-245

(-) Exons   (0, 0)

(no "Exon" information available for 1Y65)

(-) Sequences/Alignments

Asymmetric/Biological 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:330
 aligned with NAGZ_VIBCH | Q9KU37 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                             1                                                                                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
           NAGZ_VIBCH     - -MGPLWLDVAGYELSAEDREILQHPTVGGVILFGRNYHDNQQLLALNKAIRQAAKRPILIGVDQEGGRVQRFREGFSRIPPAQYYARAENGVELAEQGGWLMAAELIAHDVDLSFAPVLDMGFACKAIGNRAFGEDVQTVLKHSSAFLRGMKAVGMATTGKHFPGHGAVIADSHLETPYDERETIAQDMAIFRAQIEAGVLDAMMPAHVVYPHYDAQPASGSSYWLKQVLREELGFKGIVFSDDLSMEGAAVMGGPVERSHQALVAGCDMILICNKREAAVEVLDNLPIMEVPQAEALLKKQQFSYSELKRLERWQQASANMQRLIEQFS 329
               SCOP domains d1y65a_ A: Beta-hexosaminidase NagZ                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1y65A00 A:0-329  [code=3.20.20.300, no name defined]                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee.......hhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhh...eeee.eee..ee..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhh...ee.............hhhhh...hhhhhhhhhhhhhhhhhhh....eeeee.....................hhhhhhhhhhhhhhh...eeee...........hhhhhhhhhh...........eeeeee.....hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F3------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1y65 A   0 SLGPLWLDVAGYELSAEDREILQHPTVGGVILFGRNYHDNQQLLALNKAIRQAAKRPILIGVDQEGGRVQRFREGFSRIPPAQYYARAENGVELAEQGGWLMAAELIAHDVDLSFAPVLDMGFACKAIGNRAFGEDVQTVLKHSSAFLRGMKAVGMATTGKHFPGHGAVIADSHLETPYDERETIAQDMAIFRAQIEAGVLDAMMPAHVVYPHYDAQPASGSSYWLKQVLREELGFKGIVFSDDLSMEGAAVMGGPVERSHQALVAGCDMILICNKREAAVEVLDNLPIMEVPQAEALLKKQQFSYSELKRLERWQQASANMQRLIEQFS 329
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y65)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NAGZ_VIBCH | Q9KU37)
molecular function
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    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:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
    GO:0009273    peptidoglycan-based cell wall biogenesis    The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:115 - Pro A:116   [ RasMol ]  
    Lys A:160 - His A:161   [ RasMol ]  
    Phe A:162 - Pro A:163   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y65
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NAGZ_VIBCH | Q9KU37
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.52
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NAGZ_VIBCH | Q9KU37
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NAGZ_VIBCH | Q9KU371tr9 2oxn 3gs6 3gsm

(-) Related Entries Specified in the PDB File

1tr9 NATIVE STRUCTURE OF THE SAME PROTEIN RELATED ID: NYSGXRC-T1608 RELATED DB: TARGETDB