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(-) Description

Authors :  D. R. Knighton, Y. Deng, B. Murray, C. Guo, J. Piraino, J. Westwick, C. Zh J. Lamerdin, E. Dagostino, C. -M. Loi, M. Zager, E. Kraynov, J. Christe R. Martinez, S. Kephart, J. Marakovits, S. Karlicek, S. Bergqvist, T.
Date :  03 Feb 10  (Deposition) - 19 May 10  (Release) - 02 Jun 10  (Revision)
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Nucleotide-Binding Atp-Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  B. Murray, C. Guo, J. Piraino, J. Westwick, C. Zhang, J. Lamerdin, E. Dagostino, D. R. Knighton, C. -M. Loi, M. Zager, E. Kraynov, I. Popoff, J. Christensen, R. Martinez, S. Kephart, J. Marakovits, S. Karlicek, S. Bergqvist, T. Smeal
Small-Molecule P21-Activated Kinase Inhibitor Pf- 3758309 I A Potent Inhibitor Of Oncogenic Signaling And Tumor Growth.
Proc. Natl. Acad. Sci. Usa V. 107 9446 2010
PubMed-ID: 20439741  |  Reference-DOI: 10.1073/PNAS.0911863107

(-) Compounds

    EC Number2.7.11.1
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentKINASE DOMAIN, RESIDUES 296-591
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsS474 IS PHOSPHORYLATED
    SynonymP21-ACTIVATED KINASE 4, PAK-4

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
1AC1SOFTWARESER A:331 , ASP A:440 , LYS A:442 , X4Z A:1593 , HOH A:2079 , HOH A:2141BINDING SITE FOR RESIDUE GOL A1591
2AC2SOFTWARETHR A:332 , LYS A:350 , MET A:352 , GLU A:366 , ASP A:458 , PHE A:459 , GLY A:460 , HOH A:2016 , HOH A:2069BINDING SITE FOR RESIDUE GOL A1592
3AC3SOFTWAREILE A:327 , GLY A:328 , GLY A:330 , THR A:332 , GLY A:333 , VAL A:335 , ALA A:348 , LYS A:350 , MET A:395 , GLU A:396 , PHE A:397 , LEU A:398 , GLU A:399 , GLY A:401 , ASP A:444 , ASP A:458 , GOL A:1591 , HOH A:2142 , HOH A:2143 , HOH A:2144BINDING SITE FOR RESIDUE X4Z A1593

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X4Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X4Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X4Z)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PAK4_HUMAN327-351  1A:327-351

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:292
 aligned with PAK4_HUMAN | O96013 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:292
                                   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588  
               SCOP domains d2x4za_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Pkinase-2x4zA01 A:322-572                                                                                                                                                                                                                                  ------------------ Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------PROTEIN_KINASE_ATP       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:299-366 UniProt: 222-366 [INCOMPLETE]              Exon 1.6  PDB: A:367-411 UniProt: 367-411    ------------------------------------------Exon 1.8  PDB: A:454-495 UniProt: 454-495 Exon 1.9  PDB: A:496-540 UniProt: 496-540    Exon 1.10  PDB: A:541-590 UniProt: 541-591         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:411-453 UniProt: 411-453  ----------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                                   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468     | 478       488       498       508       518       528       538       548       558       568       578       588  

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X4Z)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
Clan: PKinase (934)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAK4_HUMAN | O96013)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0004702    signal transducer, downstream of receptor, with serine/threonine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: 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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071407    cellular response to organic cyclic compound    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0060996    dendritic spine development    The process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    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:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.


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 Related Entries

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

        PAK4_HUMAN | O960132bva 2cdz 2j0i 2ov2 2q0n 4app 4fie 4fif 4fig 4fih 4fii 4fij 4jdh 4jdi 4jdj 4jdk 4l67 4njd 4o0v 4o0x 4o0y 4xbr 4xbu 5bms 5i0b

(-) Related Entries Specified in the PDB File