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 DROSOPHILA CRYPROCHROME
 
Authors :  A. Berndt, E. Wolf
Date :  03 Apr 13  (Deposition) - 26 Jun 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Photoreceptor, Fad, Circadian Clock Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Czarna, A. Berndt, H. R. Singh, A. Grudziecki, A. G. Ladurner, G. Timinszky, A. Kramer, E. Wolf
Structures Of Drosophila Cryptochrome And Mouse Cryptochrome1 Provide Insight Into Circadian Function.
Cell(Cambridge, Mass. ) V. 153 1394 2013
PubMed-ID: 23746849  |  Reference-DOI: 10.1016/J.CELL.2013.05.011

(-) Compounds

Molecule 1 - CRYPTOCHROME-1
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: CRY, CG3772
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: DMCRY1, DCRY, BLUE LIGHT PHOTORECEPTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:265 , SER A:267 , LEU A:270 , GLN A:311 , LEU A:312 , TRP A:314 , ARG A:315 , PHE A:318 , TRP A:375 , HIS A:378 , ARG A:381 , ASN A:382 , ASP A:410 , ALA A:411 , ASP A:412 , VAL A:415 , CYS A:416 , ASN A:419 , HOH A:707 , HOH A:710BINDING SITE FOR RESIDUE FAD A 601
2AC2SOFTWAREARG B:237 , SER B:265 , SER B:267 , LEU B:270 , GLN B:311 , LEU B:312 , TRP B:314 , ARG B:315 , TRP B:375 , HIS B:378 , ARG B:381 , ASN B:382 , LEU B:408 , ASP B:410 , ALA B:411 , ASP B:412 , VAL B:415 , CYS B:416 , ASN B:419 , PHE B:534BINDING SITE FOR RESIDUE FAD B 601

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:296 -B:296

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:252 -Asn A:253
2Gly A:392 -Leu A:393
3Val B:297 -Arg B:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K03)

(-) Exons   (0, 0)

(no "Exon" information available for 4K03)

(-) 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:529
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhhhh........eeeeeeee..........hhhhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhh......hhhhhhhhhhhh....................hhhhhhhhh......hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhh...hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh.......................hhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k03 A   4 RGANVIWFRHGLRLHDNPALLAALADKDQGIALIPVFIFDGESAGTKNVGYNRMRFLLDSLQDIDDQLQAATDGRGRLLVFEGEPAYIFRRLHEQVRLHRICIEQDCEPIWNERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTVQIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNVYGDAKINWRGGETQALLLLDERLKVEQHAFERGFYLPNQALPNIHDSPKSMSAHLRFGCLSVRRFYWSVHDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTMSVNNPNYDRMEGNDICLSIPWAKPNENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTVATFLTRGGLWQSWEHGLQHFLKYLLDADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALAKRLDPDGTYIKQYVPELMNVPKEFVHEPWRMSAEQQEQYECLIGVHYPERIIDLSMAVKRNMLAMKSLRNSLITPPPHCRPSNEEEVRQFFWL 537
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213|      228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528         
                                                                                                                                                                                                                                           213|                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                            219                                                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhheeeeee........hhhhhhhhh......eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhh......hhhhhhhhhhhh....................hhhhhhhh.......hhhhhh................hhhhhhhhhhhhhhhhhhhhhh..................hhhhhhh...hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh........................hhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh...........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k03 B  -5 SSLVAAMATRGANVIWFRHGLRLHDNPALLAALADKDQGIALIPVFIFDGESAGTKNVGYNRMRFLLDSLQDIDDQLQAATDGRGRLLVFEGEPAYIFRRLHEQVRLHRICIEQDCEPIWNERDESIRSLCRELNIDFVEKVSHTLWDPQLVIETNGGIPPLTYQMFLHTVQIIGLPPRPTADARLEDATFVELDPEFCRSLKLFEQLPTPEHFNVYGDNMGFLAKINWRGGETQALLLLDERLKVEQHAFERGFYLPNQALPNIHDSPKSMSAHLRFGCLSVRRFYWSVHDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTMSVNNPNYDRMEGNDICLSIPWAKPNENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTVATFLTRGGLWQSWEHGLQHFLKYLLDADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALAKRLDPDGTYIKQYVPELMNVPKEFVHEPWRMSAEQQEQYECLIGVHYPERIIDLSMAVKRNMLAMKSLRNSLITPPPHCRPSNEEEVRQFFWL 537
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534
   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 4K03)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K03)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K03)

(-) Gene Ontology  (36, 36)

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
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:392 - Leu A:393   [ RasMol ]  
    Pro A:252 - Asn A:253   [ RasMol ]  
    Val B:297 - Arg B:298   [ 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
  4k03
    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
  CRY1_DROME | O77059
    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)
  (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
  CRY1_DROME | O77059
    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
        CRY1_DROME | O77059: 4gu5 4jzy

(-) Related Entries Specified in the PDB File

4jzy DROSOPHILA CRYPTOCHROME
4k0r MOUSE CRYPTOCHROME1