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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE T198A MUTANT OF PFPK5
 
Authors :  S. Holton, A. Merckx, D. Burgess, C. Doerig, M. Noble, J. Endicott
Date :  26 Mar 04  (Deposition) - 31 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Serine/Threonine-Protein Kinase, Atp-Binding, Phosphorylation, Cdk (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Holton, A. Merckx, D. Burgess, C. Doerig, M. Noble, J. Endicott
Structures Of P. Falciparum Pfpk5 Test The Cdk Regulation Paradigm And Suggest Mechanisms Of Small Molecule Inhibition
Structure V. 11 1329 2003
PubMed-ID: 14604523  |  Reference-DOI: 10.1016/J.STR.2003.09.020

(-) Compounds

Molecule 1 - CELL DIVISION CONTROL PROTEIN 2 HOMOLOG
    ChainsA, B
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid5833
    SynonymPFPK5

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1V0B)

(-) Sites  (0, 0)

(no "Site" information available for 1V0B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V0B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V0B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V0B)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDC2H_PLAFK10-32
 
  2A:10-32
B:10-32
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDC2H_PLAFK121-133
 
  2A:121-133
B:121-133
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDC2H_PLAFK10-32
 
  1A:10-32
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDC2H_PLAFK121-133
 
  1A:121-133
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDC2H_PLAFK10-32
 
  1-
B:10-32
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDC2H_PLAFK121-133
 
  1-
B:121-133

(-) Exons   (0, 0)

(no "Exon" information available for 1V0B)

(-) 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:287
 aligned with CDC2H_PLAFK | Q07785 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       
          CDC2H_PLAFK     1 MEKYHGLEKIGEGTYGVVYKAQNNYGETFALKKIRLEKEDEGIPSTTIREISILKELKHSNIVKLYDVIHTKKRLVLVFEHLDQDLKKLLDVCEGGLESVTAKSFLLQLLNGIAYCHDRRVLHRDLKPQNLLINREGELKIADFGLARAFGIPVRKYTHEVVTLWYRAPDVLMGSKKYSTTIDIWSVGCIFAEMVNGTPLFPGVSEADQLMRIFRILGTPNSKNWPNVTELPKYDPNFTVYEPLPWESFLKGLDESGIDLLSKMLKLDPNQRITAKQALEHAYFKEN 287
               SCOP domains d1v0ba_ A: Cyclin-dependent PK, CDK2                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1v0bA01 A:1-83 Phosphorylase Kinase; domain 1                                      1v0bA02 A:84-287 Transferase(Phosphotransferase) domain 1                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..eeeeeee.....eeeeee..........hhhhhhhhhhhhhh.......eeeeeee..eeeeee....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhhh....hhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhhh...hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PROTEIN_KINASE_ATP     ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v0b A   1 MEKYHGLEKIGEGTYGVVYKAQNNYGETFALKKIRLEKEDEGIPSTTIREISILKELKHSNIVKLYDVIHTKKRLVLVFEHLDQDLKKLLDVCEGGLESVTAKSFLLQLLNGIAYCHDRRVLHRDLKPQNLLINREGELKIADFGLARAFGIPVRKYTHEVVTLWYRAPDVLMGSKKYSTTIDIWSVGCIFAEMVNGAPLFPGVSEADQLMRIFRILGTPNSKNWPNVTELPKYDPNFTVYEPLPWESFLKGLDESGIDLLSKMLKLDPNQRITAKQALEHAYFKEN 287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with CDC2H_PLAFK | Q07785 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:285
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282     
          CDC2H_PLAFK     3 KYHGLEKIGEGTYGVVYKAQNNYGETFALKKIRLEKEDEGIPSTTIREISILKELKHSNIVKLYDVIHTKKRLVLVFEHLDQDLKKLLDVCEGGLESVTAKSFLLQLLNGIAYCHDRRVLHRDLKPQNLLINREGELKIADFGLARAFGIPVRKYTHEVVTLWYRAPDVLMGSKKYSTTIDIWSVGCIFAEMVNGTPLFPGVSEADQLMRIFRILGTPNSKNWPNVTELPKYDPNFTVYEPLPWESFLKGLDESGIDLLSKMLKLDPNQRITAKQALEHAYFKEN 287
               SCOP domains d1v0bb_ B: Cyclin-dependent PK,              CDK2                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1v0bB01 B:3-83 Phosphorylase Kin             ase; domain 1                       1v0bB02 B:84-287 Transferase(Phosphotransferase) domain 1                                                                                                                                                    CATH domains
           Pfam domains (1) -Pkinase-1v0bB01 B:4-284                                                                                                                                                                                                                                                                  --- Pfam domains (1)
           Pfam domains (2) -Pkinase-1v0bB02 B:4-284                                                                                                                                                                                                                                                                  --- Pfam domains (2)
         Sec.struct. author .eeeeeeeee....eeeeeee....eeeeeee-------------hhhhhhhhhh.......eeeeee....eeeee....eehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee...hhhhhh.----------......hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PROTEIN_KINASE_ATP     ----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v0b B   3 KYHGLEKIGEGTYGVVYKAQNNYGETFALKKI-------------IREISILKELKHSNIVKLYDVIHTKKRLVLVFEHLDQDLKKLLDVCEGGLESVTAKSFLLQLLNGIAYCHDRRVLHRDLKPQNLLINREGELKIADFGLARAFG----------VTLWYRAPDVLMGSKKYSTTIDIWSVGCIFAEMVNGAPLFPGVSEADQLMRIFRILGTPNSKNWPNVTELPKYDPNFTVYEPLPWESFLKGLDESGIDLLSKMLKLDPNQRITAKQALEHAYFKEN 287
                                    12        22        32 |       -     |  52        62        72        82        92       102       112       122       132       142        |-       162       172       182       192       202       212       222       232       242       252       262       272       282     
                                                          34            48                                                                                                    151        162                                                                                                                             

   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CDC2H_PLAFK | Q07785)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008353    RNA polymerase II carboxy-terminal domain kinase activity    Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.
    GO:0004693    cyclin-dependent protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK).
    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.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
(no "Ligands, Modified Residues, Ions" information available for 1v0b)
 
  Sites
(no "Sites" information available for 1v0b)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v0b)
 
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
  1v0b
    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
  CDC2H_PLAFK | Q07785
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.-
    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
  CDC2H_PLAFK | Q07785
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CDC2H_PLAFK | Q077851lch 1ob3 1v0o 1v0p

(-) Related Entries Specified in the PDB File

1lch THEORETICAL MODEL OF CELL DIVISION CONTROL PROTEIN LIKEPROTEIN KINASE FROM HUMAN MALARIA PARASITE PLASMODIUMFALCIPARUM
1ob3 STRUCTURE OF P. FALCIPARUM PFPK5