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(-) Description

Title :  CRYSTAL STRUCTURE OF PIM1 WITH QUERCETAGETIN
 
Authors :  S. Holder, M. Zemskova, C. Zhang, M. Tabrizizad, R. Bremer, J. W. Neidigh, M. B. Lilly
Date :  06 Dec 06  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A
Keywords :  Pim1, Quercetagetin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Holder, M. Zemskova, C. Zhang, M. Tabrizizad, R. Bremer, J. W. Neidigh, M. B. Lilly
Characterization Of A Potent And Selective Small-Molecule Inhibitor Of The Pim1 Kinase.
Mol. Cancer Ther. V. 6 163 2007
PubMed-ID: 17218638  |  Reference-DOI: 10.1158/1535-7163.MCT-06-0397
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN
    GenePIM1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
2MYU1Ligand/Ion3,5,6,7-TETRAHYDROXY-2-(3,4-DIHYDROXYPHENYL)-4H-CHROMEN-4-ONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:130 , ILE A:133 , THR A:134 , ASP A:170 , ASP A:234 , GLY A:238 , ASP A:239BINDING SITE FOR RESIDUE IMD A 401
2AC2SOFTWAREPHE A:49 , GLU A:171 , ASN A:172 , ILE A:185 , MYU A:501BINDING SITE FOR RESIDUE IMD A 402
3AC3SOFTWARELEU A:44 , ALA A:65 , LYS A:67 , GLU A:89 , ILE A:104 , LEU A:120 , GLU A:121 , ARG A:122 , VAL A:126 , LEU A:174 , ILE A:185 , ASP A:186 , IMD A:402 , HOH A:561BINDING SITE FOR RESIDUE MYU A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O64)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:124 -Pro A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041004Y144HPIM1_HUMANUnclassified  ---AY53H
2UniProtVAR_041005E215QPIM1_HUMANPolymorphism  ---AE124Q
3UniProtVAR_041006E226KPIM1_HUMANPolymorphism  ---AE135K
4UniProtVAR_041007E233DPIM1_HUMANPolymorphism  ---AE142D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PIM1_HUMAN135-158  1A:44-67
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PIM1_HUMAN254-266  1A:163-175

(-) Exons   (0, 0)

(no "Exon" information available for 2O64)

(-) 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:274
 aligned with PIM1_HUMAN | P11309 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:274
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393    
           PIM1_HUMAN   124 PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHS 397
               SCOP domains d2o64a_ A: Proto-oncogene serine/threonine-protein kinase Pim-1                                                                                                                                                                                                                    SCOP domains
               CATH domains 2o64A01 A:33-124 Phosphorylase Kinase; domain 1                                             2o64A02 A:125-306 Transferase(Phosphotransferase) domain 1                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeeee.....eeeeeeee......eee.....eeehhhhhhhhhh........eeeeee...eeeeeee....eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------H----------------------------------------------------------------------Q----------K------D-------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o64 A  33 PLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHS 306
                                    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       292       302    

   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  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O64)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIM1_HUMAN | P11309)
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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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: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:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0030212    hyaluronan metabolic process    The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:0031659    positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle    Any process that activates or increases the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity contributing to the G1/S transition of the cell cycle.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0070561    vitamin D receptor signaling pathway    The series of molecular signals generated as a consequence of a vitamin D receptor binding to one of its physiological ligands.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PIM1_HUMAN | P113091xqz 1xr1 1xws 1yhs 1yi3 1yi4 1ywv 1yxs 1yxt 1yxu 1yxv 1yxx 2bik 2bil 2bzh 2bzi 2bzj 2bzk 2c3i 2j2i 2o3p 2o63 2o65 2obj 2oi4 2xix 2xiy 2xiz 2xj0 2xj1 2xj2 3a99 3bgp 3bgq 3bgz 3bwf 3c4e 3cxw 3cy2 3cy3 3dcv 3f2a 3jpv 3jxw 3jy0 3jya 3ma3 3qf9 3r00 3r01 3r02 3r04 3t9i 3uix 3umw 3umx 3vbq 3vbt 3vbv 3vbw 3vbx 3vby 3vc4 3we8 4a7c 4alu 4alv 4alw 4as0 4bzn 4bzo 4dtk 4enx 4eny 4gw8 4i41 4iaa 4jx3 4jx7 4k0y 4k18 4k1b 4ll5 4lm5 4lmu 4mbi 4mbl 4med 4mta 4n6y 4n6z 4n70 4rbl 4rc2 4rc3 4rc4 4rpv 4ty1 4wrs 4wsy 4wt6 4xh6 4xhk 5c1q 5dgz 5dhj 5dia 5dwr 5eol 5iis 5ipj 5kzi 5v82

(-) Related Entries Specified in the PDB File

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