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 :  CRYSTAL STRUCTURE OF PUTATIVE BETA-LACTAMASE INHIBITOR PROTEIN (NP_721579.1) FROM STREPTOCOCCUS MUTANS AT 1.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 May 08  (Deposition) - 08 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Np_721579. 1, Putative Beta-Lactamase Inhibitor Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Beta-Lactamase Inhibitor Protein (Np_721579. 1) From Streptococcus Mutans At 1. 40 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE BETA-LACTAMASE INHIBITOR PROTEIN
    Atcc: 25175
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Vector Type: PLASMID
    Gene: NP_721579.1, SMU_1196C
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS MUTANS
    Organism Taxid: 1309
    Strain: CLARKE [NCTC 10449]'

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:163 , SER A:165 , LYS A:168 , GLU A:170 , HOH A:347BINDING SITE FOR RESIDUE ACT A 1
2AC2SOFTWAREGLU A:87 , GLN A:88 , ASP A:97 , TYR A:99BINDING SITE FOR RESIDUE EDO A 2
3AC3SOFTWAREARG A:120 , TYR A:147 , LEU A:160 , HOH A:231 , HOH A:241 , HOH A:249 , HOH A:288BINDING SITE FOR RESIDUE EDO A 3
4AC4SOFTWAREGLU A:140 , LYS A:142 , GLU A:145 , LYS A:149 , HOH A:248 , HOH A:353BINDING SITE FOR RESIDUE EDO A 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D4E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D4E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D4E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D4E)

(-) Exons   (0, 0)

(no "Exon" information available for 3D4E)

(-) 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:162
 aligned with Q8DTX1_STRMU | Q8DTX1 from UniProtKB/TrEMBL  Length:206

    Alignment length:162
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  
         Q8DTX1_STRMU    45 KTENLDFRLSFNKIKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKVVEKLGEPDVLSQSMSSDKEEMQTVWSSGIKTKSSSATIELYFENGLLKNKTQKDLE 206
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh...............hhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeee..........hhhhhhhh....hhhhhhhhhh...eeeeee....eeeeeee...........eeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d4e A  45 KTENLDFRLSFNKIKVTTDQNHFSGGTSIEQLKQWFGDPNKSEQRNAGNITLDSYTWVKDGAVINAQLYKNSTVARSISNFSFSREAKIGKEDYDELKIGESYKKIVEKLGEPDVLSQSmSSDKEEmQTVWSSGIKTKSSSATIELYFENGLLKNKTQKDLE 206
                                    54        64        74        84        94       104       114       124       134       144       154       164      |174       184       194       204  
                                                                                                                                                 164-MSE  |                                   
                                                                                                                                                        171-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 3D4E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D4E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D4E)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3D4E)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3d4e)
 

(-) 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
  3d4e
    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
  Q8DTX1_STRMU | Q8DTX1
    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)
  (no 'Enzyme Classificator' available)
    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
  Q8DTX1_STRMU | Q8DTX1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3D4E)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3D4E)