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(-) Description

Title :  HUMAN HSP90-BETA WITH PU3 (9-BUTYL-8(3,4,5-TRIMETHOXY-BENZYL)-9H-PURIN-6-YLAMINE)
 
Authors :  L. Wright, X. Barril, B. Dymock, L. Sheridan, A. Surgenor, M. Beswick, M. Drysdale, A. Collier, A. Massey, N. Davies, A. Fink, C. Fromont, W. A K. Boxall, S. Sharp, P. Workman, R. E. Hubbard
Date :  02 Mar 04  (Deposition) - 17 Aug 04  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Hsp90, Atpase, Pu3, Chaperone, Atp-Binding, Heat Shock (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Wright, X. Barril, B. Dymock, L. Sheridan, A. Surgenor, M. Beswick, M. Drysdale, A. Collier, A. Massey, N. Davies, A. Fink, C. Fromont, W. Aherne, K. Boxall, S. Sharp, P. Workman, R. E. Hubbard
Structure-Activity Relationships In Purine-Based Inhibitor Binding To Hsp90 Isoforms
Chem. Biol. V. 11 775 2004
PubMed-ID: 15217611  |  Reference-DOI: 10.1016/J.CHEMBIOL.2004.03.033

(-) Compounds

Molecule 1 - HEAT SHOCK PROTEIN HSP 90-BETA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET19
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentN-TERMINAL DOMAIN, RESIDUES 1-220
    OrganSKIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCLONED FROM IMAGE:3687913
    SynonymHSP 84, HSP 90
    TissueMELANOMA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PU31Ligand/Ion9-BUTYL-8-(3,4,5-TRIMETHOXYBENZYL)-9H-PURIN-6-AMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:51 , ALA A:55 , ASP A:93 , MET A:98 , LEU A:107 , ALA A:111 , PHE A:138 , TYR A:139 , VAL A:150 , THR A:184 , HOH A:2089 , HOH A:2152 , HOH A:2153 , HOH A:2154BINDING SITE FOR RESIDUE PU3 A1224

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.HS90B_HUMAN33-42  1A:38-47

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003716461aENSE00001361028chr6:44214824-44214932109HS90B_HUMAN-00--
1.3bENST000003716463bENSE00002201694chr6:44216367-44216513147HS90B_HUMAN1-49491A:16-5439
1.4bENST000003716464bENSE00002189486chr6:44217114-44217320207HS90B_HUMAN50-118691A:55-12369
1.5aENST000003716465aENSE00002183060chr6:44217412-44217571160HS90B_HUMAN119-172541A:124-17754
1.6ENST000003716466ENSE00002150570chr6:44217758-44217891134HS90B_HUMAN172-216451A:177-22145
1.7ENST000003716467ENSE00002189784chr6:44218028-44218336309HS90B_HUMAN217-3191031A:222-2265
1.8ENST000003716468ENSE00002147387chr6:44218785-44218950166HS90B_HUMAN320-375560--
1.9ENST000003716469ENSE00001140344chr6:44219155-44219345191HS90B_HUMAN375-438640--
1.10ENST0000037164610ENSE00001140336chr6:44219474-44219621148HS90B_HUMAN439-488500--
1.11dENST0000037164611dENSE00000974672chr6:44219736-44220004269HS90B_HUMAN488-577900--
1.12ENST0000037164612ENSE00000974673chr6:44220782-44221115334HS90B_HUMAN578-6891120--
1.13aENST0000037164613aENSE00001427294chr6:44221226-44221620395HS90B_HUMAN689-724360--

(-) 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:211
 aligned with HS90B_HUMAN | P08238 from UniProtKB/Swiss-Prot  Length:724

    Alignment length:211
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
          HS90B_HUMAN    11 EVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKER 221
               SCOP domains d1uyma_ A: HSP90                                                                                                                                                                                                    SCOP domains
               CATH domains 1uymA00 A:16-226  [code=3.30.565.10, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------HATPase_c-1uymA01 A:40-193                                                                                                                                --HSP90-1uymA02 A:196-226         Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhh......eeeeee....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee........eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------HSP90     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:16-54 UniProt: 1-49  Exon 1.4b  PDB: A:55-123 UniProt: 50-118                             Exon 1.5a  PDB: A:124-177 UniProt: 119-172            --------------------------------------------1.7   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:177-221 UniProt: 172-216    ----- Transcript 1 (2)
                 1uym A  16 EVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKER 226
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225 

   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  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (56, 56)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HS90B_HUMAN | P08238)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0002135    CTP binding    Interacting selectively and non-covalently with CTP, cytidine 5'-triphosphate.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0023026    MHC class II protein complex binding    Interacting selectively and non-covalently with the class II major histocompatibility complex.
    GO:0030911    TPR domain binding    Interacting selectively and non-covalently with a tetratricopeptide repeat (TPR) domain of a protein, the consensus sequence of which is defined by a pattern of small and large hydrophobic amino acids and a structure composed of helices.
    GO:0002134    UTP binding    Interacting selectively and non-covalently with UTP, uridine 5'-triphosphate.
    GO:0032564    dATP binding    Interacting selectively and non-covalently with dATP, deoxyadenosine triphosphate.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0030235    nitric-oxide synthase regulator activity    Modulates the activity of nitric oxide synthase.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019887    protein kinase regulator activity    Modulates the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0017098    sulfonylurea receptor binding    Interacting selectively and non-covalently with the sulfonylurea receptor, a regulatory subunit of the ATP-sensitive potassium ion channel.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0071353    cellular response to interleukin-4    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 interleukin-4 stimulus.
    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: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:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0032435    negative regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0045793    positive regulation of cell size    Any process that increases cell size.
    GO:0045429    positive regulation of nitric oxide biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0033160    positive regulation of protein import into nucleus, translocation    Any process that activates or increases the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0060334    regulation of interferon-gamma-mediated signaling pathway    Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
    GO:0031396    regulation of protein ubiquitination    Any process that modulates the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0060338    regulation of type I interferon-mediated signaling pathway    Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
    GO:0010033    response to organic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0009651    response to salt stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0006986    response to unfolded protein    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
    GO:0097435    supramolecular fiber organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0008180    COP9 signalosome    A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016234    inclusion body    A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HS90B_HUMAN | P082381qz2 2l6j 3fwv 3nmq 3pry 3uq3 5fwk 5fwl 5fwm 5fwp

(-) Related Entries Specified in the PDB File

1byq HSP90 N-TERMINAL DOMAIN BOUND TO ADP-MG
1osf HUMAN HSP90 IN COMPLEX WITH 17-DESMETHOXY- 17-N,N- DIMETHYLAMINOETHYLAMINO-GELDANAMYCIN
1uy6 HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(3,4,5-TRIMETHOXY-BENZYL)-9H-PURIN- 6-YLAMINE
1uy7 HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(4-METHOXY-BENZYL)-9H-PURIN-6- YLAMINE
1uy8 HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(3-TRIMETHOXY-BENZYL)-9H-PURIN- 6YLAMINE
1uy9 HUMAN HSP90-ALPHA WITH 8-BENZO[1,3]DIOXOL-,5-YLMETHYL-9-BUTYL- 9H- PURIN-6-YLAMINE
1uyc HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(2,5-DIMETHOXY-BENZYL)-9H-PURIN-6- YLAMINE
1uyd HUMAN HSP90-ALPHA WITH 9-BUTYL-8- (2-CHLORO-3,4,5-TRIMETHOXY-BENZYL) -9H-PURIN-6-YLAMINE
1uye HUMAN HSP90-ALPHA WITH 8-(2-CHLORO-3,4,5-TRIMETHOXY-BENZYL) -9-PENT- 4-YLNYL-9H-PURIN-6-YLAMINE
1uyf HUMAN HSP90-ALPHA WITH 8-(2-CHLORO-3,4,5-TRIMETHOXY-BENZYL) -2- FLUORO-9-PENT-4-YLNYL-9H-PURIN-6-YLAMINE
1uyg HUMAN HSP90-ALPHA WITH 8-(2,5-DIMETHOXY-BENZYL)-2-FLUORO-9H-PURIN-6- YLAMINE
1uyh HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(2,5-DIMETHOXY-BENZYL)-2- FLUORO- 9H-PURIN-6-YLAMINE
1uyi HUMAN HSP90-ALPHA WITH 8-(2,5-DIMETHOXY-BENZYL)-2-FLUORO-9- PENT-9H- PURIN-6-YLAMINE
1uyk HUMAN HSP90-ALPHA WITH 8-BENZO[1,3]DIOXOL-,5-YLMETHYL-9-BUTYL -2- FLUORO-9H-PURIN-6-YLAMINE
1uyl STRUCTURE-ACTIVITY RELATIONSHIPS IN PURINE-BASED INHIBITOR BINDING TO HSP90 ISOFORMS
1yer HUMAN HSP90 GELDANAMYCIN-BINDING DOMAIN, "CLOSED" CONFORMATION
1yes HUMAN HSP90 GELDANAMYCIN-BINDING DOMAIN, "OPEN" CONFORMATION
1yet GELDANAMYCIN BOUND TO THE HSP90 GELDANAMYCIN- BINDING DOMAIN