Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  THE X-RAY STRUCTURE OF THE CIS-3-CHLOROACRYLIC ACID DEHALOGENASE CIS-CAAD INACTIVATED WITH (R)-OXIRANE-2-CARBOXYLATE
 
Authors :  R. M. De Jong
Date :  06 Jan 06  (Deposition) - 21 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  3-Chloroacrylic Acid Dehalogenase, 4Ot Family, Hydratase, Covalent Inhibitor, 4-Oxalocrotonate Tautomerase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. De Jong, P. Bazzacco, G. J. Poelarends, W. H. Johnson Jr. , Y. J. Kim, E. A. Burks, H. Serrano, A. M. Thunnissen, C. P. Whitman, B. W. Dijkstra
Crystal Structures Of Native And Inactivated Cis-3-Chloroacrylic Acid Dehalogenase: Structural Basis For Substrate Specificity And Inactivation By (R)-Oxirane-2-Carboxylate.
J. Biol. Chem. V. 282 2440 2007
PubMed-ID: 17121835  |  Reference-DOI: 10.1074/JBC.M608134200

(-) Compounds

Molecule 1 - CIS-3-CHLOROACRYLIC ACID DEHALOGENASE
    Chains: A
    EC Number: 3.8.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: E. COLI BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CORYNEFORM BACTERIUM
    Organism Taxid: 1728

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1LAC1Ligand/IonLACTIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1LAC3Ligand/IonLACTIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:1 , HIS A:28 , THR A:34 , LEU A:38 , HIS A:69 , ARG A:70 , ARG A:73 , TYR A:103 , GLU A:114 , HOH A:1002BINDING SITE FOR RESIDUE LAC A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FLT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FLT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FLT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FLT)

(-) Exons   (0, 0)

(no "Exon" information available for 2FLT)

(-) 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:117
 aligned with Q6VPE5_9CORY | Q6VPE5 from UniProtKB/TrEMBL  Length:150

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
         Q6VPE5_9CORY     2 PVYMVYVSQDRLTPSAKHAVAKAITDAHRGLTGTQHFLAQVNFQEQPAGNVFLGGVQQGGDTIFVHGLHREGRSADLKGQLAQRIVDDVSVAAEIDRKHIWVYFGEMPAQQMVEYGR 118
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeee.....ee..ee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeeehhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2flt A   1 PVYMVYVSQDRLTPSAKHAVAKAITDAHRGLTGTQHFLAQVNFNEQPAGNVFLGGVQQGGDTIFVHGLHREGRSADLKGQLAQRIVDDVSVAAEIDRKHIWVYFGEMPAQQMVEYGR 117
                                    10        20        30        40        50        60        70        80        90       100       110
   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 2FLT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FLT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FLT)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2FLT)

 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
    LAC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2flt)
 
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
  2flt
    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
  Q6VPE5_9CORY | Q6VPE5
    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)
  3.8.1.-
    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
  Q6VPE5_9CORY | Q6VPE5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6VPE5_9CORY | Q6VPE5: 2flz 3mf7 3mf8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2FLT)