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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN FROM HUMAN PPAR-ALPHA IN COMPLEX WITH THE AGONIST AZ 242
 
Authors :  J. F. W. Petersen, P. Cronet, R. Folmer, N. Blomberg, K. Sjoblom, U. Karlsson, E. -L. Lindstedt, K. Bamberg
Date :  09 Mar 01  (Deposition) - 09 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Anti Parallel Helix Sandwich, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Cronet, J. F. Petersen, R. Folmer, N. Blomberg, K. Sjoblom, U. Karlsson, E. L. Lindstedt, K. Bamberg
Structure Of The Pparalpha And -Gamma Ligand Binding Domain In Complex With Az 242; Ligand Selectivity And Agonist Activation In The Ppar Family.
Structure V. 9 699 2001
PubMed-ID: 11587644  |  Reference-DOI: 10.1016/S0969-2126(01)00634-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentLIGAND BINDING DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPPAR-ALPHA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1AZ21Ligand/Ion(2S)-2-ETHOXY-3-[4-(2-{4-[(METHYLSULFONYL)OXY]PHENYL}ETHOXY)PHENYL]PROPANOIC ACID
2CPQ1Ligand/IonN,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
3NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:398 , LYS A:448 , GLU A:451 , SER A:452 , ALA A:454BINDING SITE FOR RESIDUE NA A 102
2AC2SOFTWAREILE A:241 , LEU A:247 , PHE A:273 , CYS A:275 , CYS A:276 , SER A:280 , TYR A:314 , MET A:330 , VAL A:332 , ILE A:339 , MET A:355 , HIS A:440 , VAL A:444 , LEU A:460 , TYR A:464BINDING SITE FOR RESIDUE AZ2 A 469
3AC3SOFTWARELYS A:204 , LYS A:208 , ARG A:348 , LEU A:410 , HIS A:411 , GLU A:451BINDING SITE FOR RESIDUE CPQ A 470

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I7G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:349 -Pro A:350

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016112V227APPARA_HUMANPolymorphism1800234AV227A
2UniProtVAR_016113A268VPPARA_HUMANPolymorphism1042311AA268V
3UniProtVAR_016114D304NPPARA_HUMANPolymorphism1800242AD304N
4UniProtVAR_050578G395RPPARA_HUMANPolymorphism2229245AG395R
5UniProtVAR_016115R409TPPARA_HUMANPolymorphism1800243AR409T

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I7G)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002627351cENSE00001411734chr22:46546499-4654655557PPARA_HUMAN-00--
1.3cENST000002627353cENSE00001046654chr22:46547791-4654787383PPARA_HUMAN-00--
1.9bENST000002627359bENSE00001434891chr22:46594239-46594488250PPARA_HUMAN1-70700--
1.10aENST0000026273510aENSE00000657264chr22:46611070-46611230161PPARA_HUMAN70-123540--
1.11ENST0000026273511ENSE00000657266chr22:46614160-46614298139PPARA_HUMAN124-170470--
1.12aENST0000026273512aENSE00000657268chr22:46615709-46615911203PPARA_HUMAN170-237681A:199-237 (gaps)39
1.13ENST0000026273513ENSE00000657269chr22:46627689-46628136448PPARA_HUMAN238-3871501A:238-387 (gaps)150
1.14cENST0000026273514cENSE00000880791chr22:46631030-466396538624PPARA_HUMAN387-468821A:387-46882

(-) 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:259
 aligned with PPARA_HUMAN | Q07869 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:270
                                   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468
          PPARA_HUMAN   199 ETADLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY 468
               SCOP domains d1i7ga_ A: Peroxisome proliferato  r activated receptor          alpha, PPAR-alpha                                                                                                                                                                                             SCOP domains
               CATH domains 1i7gA00 A:199-468 Retinoid X Rece  ptor                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..--.....eee.hhhhhhhhhh..---------...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..ee..eeeehhh.eeeehhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------A----------------------------------------V-----------------------------------N------------------------------------------------------------------------------------------R-------------T----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.12a  PDB: A:199-237 (gaps)      Exon 1.13  PDB: A:238-387 (gaps) UniProt: 238-387                                                                                                     --------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14c  PDB: A:387-468 UniProt: 387-468                                        Transcript 1 (2)
                 1i7g A 199 ETADLKSLAKRIYEAYLKNFNMNKVKARVILSG--SNNPPFVIHDMETLCMAEKTL---------QNKEAEVRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRDMY 468
                                   208       218       228  |  | 238       248     |   -     | 268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468
                                                          231  |                 254       264                                                                                                                                                                                                            
                                                             234                                                                                                                                                                                                                                          

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  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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I7G)

(-) Gene Ontology  (70, 70)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPARA_HUMAN | Q07869)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0097371    MDM2/MDM4 family protein binding    Interacting selectively and non-covalently with any isoform of the MDM2/MDM4 protein family, comprising negative regulators of p53.
    GO:0051525    NFAT protein binding    Interacting selectively and non-covalently with NFAT (nuclear factor of activated T cells) proteins, a family of transcription factors. NFAT proteins have crucial roles in the development and function of the immune system.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0001103    RNA polymerase II repressing transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0001223    transcription coactivator binding    Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0001190    transcriptional activator activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0031624    ubiquitin conjugating enzyme binding    Interacting selectively and non-covalently with a ubiquitin conjugating enzyme, any of the E2 proteins.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0035095    behavioral response to nicotine    Any process that results in a change in the behavior of an organism as a result of a nicotine stimulus.
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0070166    enamel mineralization    The process in which calcium salts, mainly carbonated hydroxyapatite, are deposited in tooth enamel.
    GO:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0015908    fatty acid transport    The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0032099    negative regulation of appetite    Any process that reduces appetite.
    GO:0045776    negative regulation of blood pressure    Any process in which the force of blood traveling through the circulatory system is decreased.
    GO:0010887    negative regulation of cholesterol storage    Any process that decreases the rate or extent of cholesterol storage. Cholesterol storage is the accumulation and maintenance in cells or tissues of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0045820    negative regulation of glycolytic process    Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:1903038    negative regulation of leukocyte cell-cell adhesion    Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte cell-cell adhesion.
    GO:0010745    negative regulation of macrophage derived foam cell differentiation    Any process that decreases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions.
    GO:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    GO:1902894    negative regulation of pri-miRNA transcription from RNA polymerase II promoter    Any process that stops, prevents or reduces the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0010871    negative regulation of receptor biosynthetic process    Any process that decreases the frequency or rate of receptor biosynthesis. Receptor biosynthesis is the collection of chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0010891    negative regulation of sequestering of triglyceride    Any process that decreases the rate, frequency or extent of sequestering of triglyceride. Triglyceride sequestration is the process of binding or confining any triester of glycerol such that it is separated from other components of a biological system.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:2000678    negative regulation of transcription regulatory region DNA binding    Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:0032000    positive regulation of fatty acid beta-oxidation    Any process that activates or increases the frequency, rate or extent of fatty acid beta-oxidation.
    GO:0046321    positive regulation of fatty acid oxidation    Any process that activates or increases the frequency, rate or extent of fatty acid oxidation.
    GO:0045722    positive regulation of gluconeogenesis    Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0072366    regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of a cellular ketone metabolic process by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0019217    regulation of fatty acid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving fatty acids.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0072363    regulation of glycolytic process by positive regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of glycolysis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0072369    regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of lipid transport by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001666    response to hypoxia    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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0032868    response to insulin    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 insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPARA_HUMAN | Q078691k7l 1kkq 2npa 2p54 2rew 2znn 3et1 3fei 3g8i 3kdt 3kdu 3sp6 3vi8 4bcr 4ci4 5azt 5hyk

(-) Related Entries Specified in the PDB File

1i7i CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF HUMAN PPAR-GAMMA IN COMPLEX WITH THE AGONIST AZ 242