Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA CHALCONE ISOMERASE AT3G55120 (ATCHI)
 
Authors :  J. P. Noel, G. V. Louie, M. E. Bowman
Date :  09 Feb 12  (Deposition) - 09 May 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Chalcone-Flavanone Isomerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. N. Ngaki, G. V. Louie, R. N. Philippe, G. Manning, F. Pojer, M. E. Bowman, L. Li, E. Larsen, E. S. Wurtele, J. P. Noel
Evolution Of The Chalcone-Isomerase Fold From Fatty-Acid Binding To Stereospecific Catalysis.
Nature V. 485 530 2012
PubMed-ID: 22622584  |  Reference-DOI: 10.1038/NATURE11009

(-) Compounds

Molecule 1 - CHALCONE--FLAVONONE ISOMERASE 1
    ChainsA, B
    EC Number5.5.1.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS8
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneAT3G55120, CFI, CHI1, T15C9_120, TT5
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymCHALCONE ISOMERASE 1, PROTEIN TRANSPARENT TESTA 5

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NO34Ligand/IonNITRATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NO32Ligand/IonNITRATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NO32Ligand/IonNITRATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:47 , THR A:59 , VAL A:106 , TYR A:117 , VAL A:208 , HOH A:1082BINDING SITE FOR RESIDUE NO3 A 301
2AC2SOFTWAREARG A:47 , PHE A:58 , LEU A:112 , GLN A:116 , TYR A:117 , LYS A:120 , HOH A:1124BINDING SITE FOR RESIDUE NO3 A 302
3AC3SOFTWAREHOH A:1159 , ARG B:1047 , PHE B:1058 , LEU B:1112 , GLN B:1116 , TYR B:1117BINDING SITE FOR RESIDUE NO3 B 1301
4AC4SOFTWAREARG B:1047 , THR B:1059 , VAL B:1106 , TYR B:1117 , VAL B:1208 , HOH B:1450BINDING SITE FOR RESIDUE NO3 B 1302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DOI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CFI1_ARATH_001 *I202VCFI1_ARATH  ---  ---A
B
I202
1202
V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CFI1_ARATH_001 *I202VCFI1_ARATH  ---  ---A
A
I202
1202
V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CFI1_ARATH_001 *I202VCFI1_ARATH  ---  ---A
B
I202
1202
V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DOI)

(-) 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:221
 aligned with CFI1_ARATH | P41088 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:221
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 
          CFI1_ARATH     15 AVTKLHVDSVTFVPSVKSPASSNPLFLGGAGVRGLDIQGKFVIFTVIGVYLEGNAVPSLSVKWKGKTTEELTESIPFFREIVTGAFEKFIKVTMKLPLTGQQYSEKVTENCVAIWKQLGLYTDCEAKAVEKFLEIFKEETFPPGSSILFALSPTGSLTVAFSKDDSIPETGIAVIENKLLAEAVLESIIGKNGVSPGTRLSVAERLSQLMMKNKDEKEVSD  235
               SCOP domains d4doia_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee..eee......eeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...eeeeeee...eehhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh..ee....eeeeee....eeeeeee..........eeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4doi A   15 AVTKLHVDSVTFVPSVKSPASSNPLFLGGAGVRGLDIQGKFVIFTVIGVYLEGNAVPSLSVKWKGKTTEELTESIPFFREIVTGAFEKFIKVTMKLPLTGQQYSEKVTENCVAIWKQLGLYTDCEAKAVEKFLEIFKEETFPPGSSILFALSPTGSLTVAFSKDDSIPETGIAVIENKLLAEAVLESIIGKNGVSPGTRLSVAERLSQLMMKNKDEKEVSD  235
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with CFI1_ARATH | P41088 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:213
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224   
          CFI1_ARATH     15 AVTKLHVDSVTFVPSVKSPASSNPLFLGGAGVRGLDIQGKFVIFTVIGVYLEGNAVPSLSVKWKGKTTEELTESIPFFREIVTGAFEKFIKVTMKLPLTGQQYSEKVTENCVAIWKQLGLYTDCEAKAVEKFLEIFKEETFPPGSSILFALSPTGSLTVAFSKDDSIPETGIAVIENKLLAEAVLESIIGKNGVSPGTRLSVAERLSQLMMKN  227
               SCOP domains d4doib_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee..eee......eeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...eeeeeee...eehhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh..ee....eeeeee....eeeeeee..........eeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4doi B 1015 AVTKLHVDSVTFVPSVKSPASSNPLFLGGAGVRGLDIQGKFVIFTVIGVYLEGNAVPSLSVKWKGKTTEELTESIPFFREIVTGAFEKFIKVTMKLPLTGQQYSEKVTENCVAIWKQLGLYTDCEAKAVEKFLEIFKEETFPPGSSILFALSPTGSLTVAFSKDDSIPETGIAVIENKLLAEAVLESIIGKNGVSPGTRLSVAERLSQLMMKN 1227
                                  1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CFI1_ARATH | P41088)
molecular function
    GO:0045430    chalcone isomerase activity    Catalysis of the reaction: a chalcone = a flavanone.
    GO:0016872    intramolecular lyase activity    The catalysis of certain rearrangements of a molecule to break or form a ring.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0009813    flavonoid biosynthetic process    The chemical reactions and pathways resulting in the formation of flavonoids, a group of phenolic derivatives containing a flavan skeleton.
    GO:0009411    response to UV    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 ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0010224    response to UV-B    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 a UV-B radiation stimulus. UV-B radiation (UV-B light) spans the wavelengths 280 to 315 nm.
    GO:0009733    response to auxin    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 auxin stimulus.
    GO:0080167    response to karrikin    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 a karrikin stimulus. Karrikins are signaling molecules in smoke from burning vegetation that trigger seed germination for many angiosperms (flowering plants).
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0042406    extrinsic component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0009705    plant-type vacuole membrane    The lipid bilayer surrounding a vacuole that retains the same shape regardless of cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this component is found in Arabidopsis thaliana.

 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
    NO3  [ 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 4doi)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) 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
  4doi
    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
  CFI1_ARATH | P41088
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.5.1.6
    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
  CFI1_ARATH | P41088
    Protein Disorder PredictionDisEMBL | 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 4DOI)

(-) Related Entries Specified in the PDB File

4dok 4dol 4doo