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 CRYPTOSPORIDIUM PARVUM CDPK1, CGD3_920
 
Authors :  A. K. Wernimont, J. D. Artz, P. Finnerty, M. Amani, A. Allali-Hassanali M. Vedadi, W. Tempel, F. Mackenzie, A. M. Edwards, C. H. Arrowsmith, C. J. Weigelt, A. Bochkarev, R. Hui, Y. H. Lin, Structural Genomics Con (Sgc)
Date :  28 Jul 09  (Deposition) - 11 Aug 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Parasite, Kinase, Cdpk, Structural Genomics, Structural Genomics Consortium, Sgc, Atp-Binding, Nucleotide-Binding, Serine/Threonine- Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, J. D. Artz, P. Finerty, Y. H. Lin, M. Amani, A. Allali-Hassani, G. Senisterra, M. Vedadi, W. Tempel, F. Mackenzie I. Chau, S. Lourido, L. D. Sibley, R. Hui
Structures Of Apicomplexan Calcium-Dependent Protein Kinase Reveal Mechanism Of Activation By Calcium.
Nat. Struct. Mol. Biol. V. 17 596 2010
PubMed-ID: 20436473  |  Reference-DOI: 10.1038/NSMB.1795

(-) Compounds

Molecule 1 - CALMODULIN-DOMAIN PROTEIN KINASE 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15MHL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 70-538
    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  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CA4Ligand/IonCALCIUM ION
3GOL6Ligand/IonGLYCEROL
4PO41Ligand/IonPHOSPHATE ION
5SRT1Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:515 , ASN A:517 , ASP A:519 , GLU A:521 , GLU A:526BINDING SITE FOR RESIDUE CA A 601
02AC2SOFTWAREASP A:393 , ASN A:395 , ASP A:397 , MET A:399 , GLU A:404 , HOH A:547BINDING SITE FOR RESIDUE CA A 602
03AC3SOFTWAREASP A:443 , ASP A:445 , SER A:447 , SER A:449 , GLU A:451 , GLU A:454BINDING SITE FOR RESIDUE CA A 603
04AC4SOFTWAREHOH A:37 , HOH A:47 , GLY A:83 , GLY A:85 , SER A:86 , PHE A:87 , GLY A:88 , VAL A:90 , LYS A:105 , GLU A:153 , TYR A:155 , ASP A:219BINDING SITE FOR RESIDUE ANP A 610
05AC5SOFTWAREGLU A:101 , TYR A:102 , GLU A:153 , LEU A:154 , THR A:377 , THR A:378 , LEU A:379BINDING SITE FOR RESIDUE GOL A 1
06AC6SOFTWARETYR A:76 , ASP A:95 , PHE A:139 , GLU A:140 , LYS A:375 , MET A:477 , HOH A:611BINDING SITE FOR RESIDUE GOL A 539
07AC7SOFTWAREGLN A:325 , ARG A:468 , VAL A:528 , GOL A:546 , HOH A:579 , HOH A:589BINDING SITE FOR RESIDUE GOL A 540
08AC8SOFTWAREASP A:481 , GLY A:484 , ILE A:486BINDING SITE FOR RESIDUE CA A 541
09AC9SOFTWAREHIS A:316 , PRO A:317 , SER A:318 , LYS A:476 , GLY A:482BINDING SITE FOR RESIDUE GOL A 542
10BC1SOFTWARETYR A:291 , PHE A:293 , ARG A:310BINDING SITE FOR RESIDUE SRT A 543
11BC2SOFTWAREHIS A:196 , ARG A:197 , ASP A:198 , ASP A:219 , GLY A:221 , SER A:223BINDING SITE FOR RESIDUE GOL A 544
12BC3SOFTWARELYS A:166 , LYS A:209BINDING SITE FOR RESIDUE PO4 A 545
13BC4SOFTWARELYS A:254 , SER A:318 , ARG A:320 , THR A:322 , GLN A:325 , ASN A:525 , GOL A:540BINDING SITE FOR RESIDUE GOL A 546

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IGO)

(-) 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:446
 aligned with A3FQ16_CRYPI | A3FQ16 from UniProtKB/TrEMBL  Length:538

    Alignment length:469
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       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         
         A3FQ16_CRYPI    69 SGTFAERYNIVCMLGKGSFGEVLKCKDRITQQEYAVKVINKASAKNKDTSTILREVELLKKLDHPNIMKLFEILEDSSSFYIVGELYTGGELFDEIIKRKRFSEHDAARIIKQVFSGITYMHKHNIVHRDLKPENILLESKEKDCDIKIIDFGLSTCFQQNTKMKDRIGTAYYIAPEVLRGTYDEKCDVWSAGVILYILLSGTPPFYGKNEYDILKRVETGKYAFDLPQWRTISDDAKDLIRKMLTFHPSLRITATQCLEHPWIQKYSSETPTISDLPSLESAMTNIRQFQAEKKLAQAALLYMASKLTTLDETKQLTEIFRKLDTNNDGMLDRDELVRGYHEFMRLKGVDSNSLIQNEGSTIEDQIDSLMPLLDMDGSGSIEYSEFIASAIDRTILLSRERMERAFKMFDKDGSGKISTKELFKLFSQADSSIQMEELESIIEQVDNNKDGEVDFNEFVEMLQNFVRN 537
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeeee....eeeeeee.....eeeeeeeehhhhh..-hhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee.............-------hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhh.--..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.-------------hhhhhhhh.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3igo A  69 QGTFAERYNIVCMLGKGSFGEVLKCKDRITQQEYAVKVINKASAKNK-TSTILREVELLKKLDHPNIMKLFEILEDSSSFYIVGELYTGGELFDEIIKRKRFSEHDAARIIKQVFSGITYMHKHNIVHRDLKPENILLESKEKDCDIKIIDFGLSTCFQQNT-------TAYYIAPEVLRGTYDEKCDVWSAGVILYILLSGTPPFYGKNEYDILKRVETGKYAFDLPQWRTISDDAKDLIRKMLTFHPSLRITATQCLEHPWIQKYSSETPTISDLPSLESAMTNIRQFQAEKKLAQAALLYMASKLTTLDETKQLTEIFRKLDTNNDGMLDRDELVRGYHEFMRLKGVDSNSLIQ--GSTIEDQIDSLMPLLDMDGSGSIEYSEFIASAIDRTILLSRERMERAFKMFDKDGSGKISTKELFKL-------------ESIIEQVDNNKDGEVDFNEFVEMLQNFVRN 537
                                    78        88        98       108      |118       128       138       148       158       168       178       188       198       208       218       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     |   -       508       518       528         
                                                                        115 |                                                                                                              230     238                                                                                                                                                                                        425  |                                                               494           508                             
                                                                          117                                                                                                                                                                                                                                                                                                                    428
   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 3IGO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IGO)

(-) Pfam Domains  (0, 0)

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

(-) 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
    ANP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SRT  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3igo)
 

(-) 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
  3igo
    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 3dfa 3mwu 3ncg 4y5q

(-) Related Entries Specified in the PDB File

3hx4 CRYSTAL STRUCTURE OF CDPK1 OF TOXOPLASMA GONDII, TGME49_ 101440, IN PRESENCE OF CALCIUM
3hzt CRYSTAL STRUCTURE OF TOXOPLASMA GONDII CDPK3, TGME49_105860