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 :  CRYPTOSPORIDIUM PARVUM CYCLIN-DEPENDENT KINASE CGD5_2510 WITH ADP BOUND.
 
Authors :  A. K. Wernimont, A. Dong, J. Lew, Y. H. Lin, A. Hassanali, C. H. Arrowsmit A. M. Edwards, J. Weigelt, C. Bountra, A. Bochkarev, R. Hui, J. D. Artz, Structural Genomics Consortium (Sgc)
Date :  16 Jun 10  (Deposition) - 28 Jul 10  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Phosphotransferase, Cyclin Dependent Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, A. Dong, J. Lew, Y. H. Lin, A. Hassanali, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, A. Bochkarev, R. Hui, J. D. Artz
Cryptosporidium Parvum Cyclin-Dependent Kinase Cgd5_2510 With Adp Bound.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RHODANESE FAMILY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CGD5_2510
    Organism Scientific: CRYPTOSPORIDIUM PARVUM
    Organism Taxid: 353152
    Strain: IOWA II

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:148 , ASN A:149 , ASP A:162 , ADP A:314BINDING SITE FOR RESIDUE MG A 312
2AC2SOFTWAREADP A:314 , HOH A:365 , HOH A:366BINDING SITE FOR RESIDUE MG A 313
3AC3SOFTWAREGLY A:30 , GLU A:31 , GLY A:32 , THR A:33 , VAL A:37 , ALA A:49 , LYS A:51 , PHE A:98 , GLU A:99 , MET A:101 , ASP A:104 , GLN A:148 , ASN A:149 , LEU A:151 , ASP A:162 , MG A:312 , MG A:313 , HOH A:320 , HOH A:333 , HOH A:365 , HOH A:366BINDING SITE FOR RESIDUE ADP A 314

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NIZ)

(-) 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:288
 aligned with Q5CRJ8_CRYPI | Q5CRJ8 from UniProtKB/TrEMBL  Length:295

    Alignment length:297
                                1                                                                                                                                                                                                                                                                                                    
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       
         Q5CRJ8_CRYPI     - ----LMEKYQKLEKVGEGTYGVVYKAKDSQGRIVALKRIRLDAEDEGIPSTAIREISLLKELHHPNIVSLIDVIHSERCLTLVFEFMEKDLKKVLDENKTGLQDSQIKIYLYQLLRGVAHCHQHRILHRDLKPQNLLINSDGALKLADFGLARAFGIPVRSYTHEVVTLWYRAPDVLMGSKKYSTSVDIWSIGCIFAEMITGKPLFPGVTDDDQLPKIFSILGTPNPREWPQVQELPLWKQRTFQVFEKKPWSSIIPGFCQEGIDLLSNMLCFDPNKRISARDAMNHPYFKDLDPQI 293
               SCOP domains d3niza_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeeeeeeeee....eeeeeee....eeeeeee.------hhhhhhhhhhhhhhhh.......eeeee.....eeeeee...eehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......---.........hhhhhh......hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh......hhhhh.hhhhhh.........hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3niz A  15 YFQGLMEKYQKLEKVGEGTYGVVYKAKDSQGRIVALKRIR------GIPSTAIREISLLKELHHPNIVSLIDVIHSERCLTLVFEFMEKDLKKVLDENKTGLQDSQIKIYLYQLLRGVAHCHQHRILHRDLKPQNLLINSDGALKLADFGLARAFGIPVR---HEVVTLWYRAPDVLMGSKKYSTSVDIWSIGCIFAEMITGKPLFPGVTDDDQLPKIFSILGTPNPREWPQVQELPLWKQRTFQVFEKKPWSSIIPGFCQEGIDLLSNMLCFDPNKRISARDAMNHPYFKDLDPQI 311
                                    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       
                                                                  54     61                                                                                                              174 178
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5CRJ8_CRYPI | Q5CRJ8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3niz)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  3niz
    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
  Q5CRJ8_CRYPI | Q5CRJ8
    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
  Q5CRJ8_CRYPI | Q5CRJ8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5CRJ8_CRYPI | Q5CRJ8: 2qkr

(-) Related Entries Specified in the PDB File

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