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

(-) Description

Title :  DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N-ACETYLGLUCOSAMINIDASE, STRH
 
Authors :  B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston
Date :  23 Jun 12  (Deposition) - 10 Jul 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Pluvinage, K. A. Stubbs, D. J. Vocadlo, A. B. Boraston
Inhibition Of The Family 20 Glycoside Hydrolase Catalytic Modules In The Streptococcus Pneumoniae Exo-Beta-D-N- Acetylglucosaminidase, Strh.
Org. Biomol. Chem. V. 11 7907 2013
PubMed-ID: 24132305  |  Reference-DOI: 10.1039/C3OB41579A

(-) Compounds

Molecule 1 - BETA-N-ACETYLHEXOSAMINIDASE
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC MODULE, RESIDUES 181-613
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: GLYCOSIDE HYDROLASE 20

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2LOG2Ligand/IonLOGNAC
3MG2Ligand/IonMAGNESIUM ION
4P151Ligand/Ion2,5,8,11,14,17-HEXAOXANONADECAN-19-OL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:196 , HIS A:297 , ASP A:360 , GLU A:361 , PHE A:415 , TRP A:439 , TYR A:469 , TYR A:482 , TRP A:517 , ASP A:519 , HOH A:2061 , HOH A:2427 , HOH A:2575BINDING SITE FOR RESIDUE LOG A1614
02AC2SOFTWARETYR A:280 , ASP A:283 , LYS A:284 , HOH A:2038 , HOH A:2174 , HOH A:2183 , HOH A:2576BINDING SITE FOR RESIDUE LOG A1615
03AC3SOFTWARETYR A:317 , TYR A:381 , TYR A:386 , HOH A:2229 , HOH A:2327 , HOH A:2577 , HOH A:2578BINDING SITE FOR RESIDUE P15 A1616
04AC4SOFTWAREASP A:259 , HOH A:2132 , HOH A:2133 , HOH A:2134 , HOH A:2135 , HOH A:2579BINDING SITE FOR RESIDUE MG A1617
05AC5SOFTWAREHOH A:2501 , HOH A:2502 , HOH A:2581 , HOH A:2582 , HOH A:2583BINDING SITE FOR RESIDUE MG A1622
06AC6SOFTWAREASN A:399 , ASP A:431 , ASN A:564 , HOH A:2222 , HOH A:2341 , HOH A:2515BINDING SITE FOR RESIDUE EDO A1618
07AC7SOFTWAREASN A:422 , SER A:423 , HOH A:2580BINDING SITE FOR RESIDUE EDO A1619
08AC8SOFTWARETYR A:260 , PRO A:521 , HOH A:2238 , HOH A:2284BINDING SITE FOR RESIDUE EDO A1620
09AC9SOFTWAREALA A:346 , LYS A:350 , HIS A:408 , GLY A:409 , HOH A:2268 , HOH A:2269 , HOH A:2273 , HOH A:2352BINDING SITE FOR RESIDUE EDO A1623
10BC1SOFTWAREASN A:181 , GLU A:182 , LYS A:183 , HOH A:2001 , HOH A:2004 , HOH A:2006BINDING SITE FOR RESIDUE EDO A1621

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AZ7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:294 -Pro A:295

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AZ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AZ7)

(-) Exons   (0, 0)

(no "Exon" information available for 4AZ7)

(-) 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:433
 aligned with STRH_STRPN | P49610 from UniProtKB/Swiss-Prot  Length:1312

    Alignment length:433
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610   
           STRH_STRPN   181 NEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKDLNRYTAESVTAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQETVNNLTLT 613
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhhhhhhhhhhh..eeeeeee.....ee.....eee..eeehhhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh....eeee..eeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhh..........eeee...........hhhhhhhh...eee.hhhhhee...........hhhhhhhhhhhh................eeeeeee........hhhhhhhhhhhhhhhh.......hhhhhhhhhh........hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4az7 A 181 NEKLAKKKIVSIDAGRKYFSPEQLKEIIDKAKHYGYTDLHLLVGNDGLRFMLDDMSITANGKTYASDDVKRAIEKGTNDYYNDPNGNHLTESQMTDLINYAKDKGIGLIPTVNSPGHMDAILNAMKELGIQNPNFSYFGKKSARTVDLDNEQAVAFTKALIDKYAAYFAKKTEIFNIGLDEYANDATDAKGWSVLQADKYYPNEGYPVKGYEKFIAYANDLARIVKSHGLKPMAFNDGIYYNSDTSFGSFDKDIIVSMWTGGWGGYDVASSKLLAEKGHQILNTNDAWYYVLGRNADGQGWYNLDQGLNGIKNTPITSVPKTEGADIPIIGGMVAAWADTPSARYSPSRLFKLMRHFANANAEYFAADYESAEQALNEVPKDLNRYTAESVTAVKEAEKAIRSLDSNLSRAQQDTIDQAIAKLQETVNNLTLT 613
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610
   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 4AZ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AZ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AZ7)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (STRH_STRPN | P49610)
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: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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LOG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P15  [ 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
    Ser A:294 - Pro A:295   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4az7
    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
  STRH_STRPN | P49610
    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)
  3.2.1.52
    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
  STRH_STRPN | P49610
    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
        STRH_STRPN | P49610: 2ltj 2yl5 2yl6 2yl8 2yl9 2yla 2yll 4az5 4az6 4azb 4azc 4azg 4azh 4azi

(-) Related Entries Specified in the PDB File

2yl5 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl6 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl8 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yl9 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yla INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
2yll INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS
4az5 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4az6 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azb DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azc DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azg DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azh DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH
4azi DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH