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

(-) Description

Title :  CRYSTAL STRUCTURE OF KINASE DOMAIN OF CALCIUM-DEPENDENT PROTEIN KINASE CGD3_920 FROM CRYPTOSPORIDIUM PARVUM
 
Authors :  A. K. Wernimont, J. Lew, Y. H. Lin, A. Hassanali, C. Khuu, Z. Alam, I. Kozi D. Cossar, A. Bochkarev, C. H. Arrowsmith, C. Bountra, M. Wilkstrom, A. M. Edwards, R. Hui, J. D. Artz, T. Xiao, Structural Genomics Conso (Sgc)
Date :  11 Jun 08  (Deposition) - 29 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Calmodulin, Kinase, Malaria, Transferase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, J. Lew, Y. H. Lin, A. Hassanali, C. Khuu, Z. Alam, I. Kozieradzki, D. Cossar, A. Bochkarev, C. H. Arrowsmith, C. Bountra M. Wilkstrom, A. M. Edwards, R. Hui, J. D. Artz, T. Xiao
Crystal Structure Of Kinase Domain Of Calcium-Dependent Protein Kinase Cgd3_920 From Cryptosporidium Parvum.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CALCIUM-DEPENDENT PROTEIN KINASE CGD3_920
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CGD3_920
    Organism Scientific: CRYPTOSPORIDIUM PARVUM
    Organism Taxid: 353152
    Strain: IOWA II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3DFA)

(-) Sites  (0, 0)

(no "Site" information available for 3DFA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DFA)

(-) 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:265
 aligned with A3FQ16_CRYPI | A3FQ16 from UniProtKB/TrEMBL  Length:538

    Alignment length:273
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333   
         A3FQ16_CRYPI    64 FVQSGSGTFAERYNIVCMLGKGSFGEVLKCKDRITQQEYAVKVINKASAKNKDTSTILREVELLKKLDHPNIMKLFEILEDSSSFYIVGELYTGGELFDEIIKRKRFSEHDAARIIKQVFSGITYMHKHNIVHRDLKPENILLESKEKDCDIKIIDFGLSTCFQQNTKMKDRIGTAYYIAPEVLRGTYDEKCDVWSAGVILYILLSGTPPFYGKNEYDILKRVETGKYAFDLPQWRTISDDAKDLIRKMLTFHPSLRITATQCLEHPWIQKYS 336
               SCOP domains d3d   faa_ A: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -3d   faA01 A:-1-87 Phosphorylase Kinase; domain 1                                            3dfaA02 A:89-267 Transferase(Phosphotransferase)     domain 1                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...---hhhhhheeeeeeeee....eeeeeee.....eeeeeeee.hhh...hhhhhhhhhhhhhhh.......eeeeee...eeeeee....-.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.ee.----.....ee...hhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfa A  -2 YFQ---GTFAERYNIVCMLGKGSFGEVLKCKDRITQQEYAVKVINKASAKNKDTSTILREVELLKKLDHPNIMKLFEILEDSSSFYIVGELYT-GELFDEIIKRKRFSEHDAARIIKQVFSGITYMHKHNIVHRDLKPENILL----KDCDIKIIDFGLSTCFQQNTKMKDRIGTAYYIAPEVLRGTYDEKCDVWSAGVILYILLSGTPPFYGKNEYDILKRVETGKYAFDLPQWRTISDDAKDLIRKMLTFHPSLRITATQCLEHPWIQKYS 267
                              |   |  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   
                              0   1                                                                                    87 |                                             137  142                                                                                                                             
                                                                                                                         89
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A3FQ16_CRYPI | A3FQ16)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.

 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
(no "Ligands, Modified Residues, Ions" information available for 3dfa)
 
  Sites
(no "Sites" information available for 3dfa)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dfa)
 

(-) 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 ](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
  3dfa
    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
  A3FQ16_CRYPI | A3FQ16
    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
  A3FQ16_CRYPI | A3FQ16
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A3FQ16_CRYPI | A3FQ16: 2wei 3igo 3mwu 3ncg 4y5q

(-) Related Entries Specified in the PDB File

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