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 B. THURINGIENSIS AIIA MUTANT F107W
 
Authors :  C. F. Liu, D. Liu, J. Momb, P. W. Thomas, A. Lajoie, G. A. Petsko, W. Fast, D
Date :  08 Feb 13  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A
Keywords :  Aiia, Lactonase, Dizinc Hydrolase, Substrate Specificity, Quorum Quenching, Beta-Hairpin Loops, N-Acyl Homoserine Lactone, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. F. Liu, D. Liu, J. Momb, P. W. Thomas, A. Lajoie, G. A. Petsko, W. Fast, D. Ringe
A Phenylalanine Clamp Controls Substrate Specificity In The Quorum-Quenching Metallo-Gamma-Lactonase From Bacillus Thuringiensis.
Biochemistry V. 52 1603 2013
PubMed-ID: 23387521  |  Reference-DOI: 10.1021/BI400050J

(-) Compounds

Molecule 1 - N-ACYL HOMOSERINE LACTONASE
    Chains: A
    EC Number: 3.1.1.81
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AIIA
    Mutation: YES
    Organism Scientific: BACILLUS THURINGIENSIS
    Organism Taxid: 1428
    Synonym: AHL-LACTONASE, HOMOSERINE LACTONE LACTONASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:108 , HIS A:109 , ASP A:191 , HIS A:235 , ZN A:302 , HOH A:401BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:104 , HIS A:106 , HIS A:169 , ASP A:191 , ZN A:301 , HOH A:401BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWARELYS A:29 , LEU A:30 , ARG A:89 , PHE A:246 , HOH A:471BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREGLU A:61 , LYS A:76 , MET A:77 , THR A:78BINDING SITE FOR RESIDUE GOL A 304
5AC5SOFTWAREHIS A:145 , ASN A:147 , LYS A:226 , HOH A:407 , HOH A:517BINDING SITE FOR RESIDUE GOL A 305
6AC6SOFTWAREALA A:115 , GLU A:152 , GLY A:153 , TYR A:165 , HOH A:411 , HOH A:424BINDING SITE FOR RESIDUE GOL A 306
7AC7SOFTWAREGLU A:61 , GLY A:62 , ASN A:65 , LEU A:74 , TYR A:249BINDING SITE FOR RESIDUE GOL A 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J5F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:246 -Pro A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J5F)

(-) Exons   (0, 0)

(no "Exon" information available for 4J5F)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeeee.hhh........eeeeeeeeeeeee..eeeee....hhhhh..............eeee.hhhhhhhhhhhhhh.hhhhh.eee....hhhhhhhhhhh....eeeehhhhhhhh.....hhhhh.....eeee...eeee..eeeee........eeeeeee...eeeeeeehhh.hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j5f A   1 MTVKKLYFIPAGRCMLDHSSVNSALTPGKLLNLPVWCYLLETEEGPILVDTGMPESAVNNEGLFNGTFVEGQILPKMTEEDRIVNILKRVGYEPDDLLYIISSHLHWDHAGGNGAFTNTPIIVQRTEYEAALHREEYMKECILPHLNYKIIEGDYEVVPGVQLLYTPGHSPGHQSLFIETEQSGSVLLTIDASYTKENFEDEVPFAGFDPELALSSIKRLKEVVKKEKPIIFFGHDIEQEKSCRVFPEYI 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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 4J5F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J5F)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
    Phe A:246 - Pro A:247   [ 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
  4j5f
    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
  AHLL_BACTU | A3FJ64
    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)
  3.1.1.81
    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
  AHLL_BACTU | A3FJ64
    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
        AHLL_BACTU | A3FJ64: 3dha 3dhb 3dhc 4j5h 5eht

(-) Related Entries Specified in the PDB File

4j5h