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(-) Description

Title :  ISOXAZOLE LIGAND BOUND TO FARNESOID X RECEPTOR (FXR)
 
Authors :  K. P. Madauss, S. P. Williams, D. N. Deaton, G. B. Wisely, R. B. Mcfadyen
Date :  23 Feb 09  (Deposition) - 07 Jul 09  (Release) - 07 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fxr, Nuclear Recptor, Activator, Alternative Splicing, Dna- Binding, Metal-Binding, Nucleus, Receptor, Repressor, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Transcription/Transcrition Activator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Y. Bass, R. D. Caldwell, J. A. Caravella, L. Chen, K. L. Creech, D. N. Deaton, K. P. Madauss, H. B. Marr, R. B. Mcfadyen, A. B. Miller, D. J. Parks, D. Todd, S. P. Williams, G. B. Wisely
Substituted Isoxazole Analogs Of Farnesoid X Receptor (Fxr) Agonist Gw4064.
Bioorg. Med. Chem. Lett. V. 19 2969 2009
PubMed-ID: 19410460  |  Reference-DOI: 10.1016/J.BMCL.2009.04.047
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BILE ACID RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentFARSENOID X RECEPTOR
    GeneNR1H4, BAR, FXR, HRR1, RIP14
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFARNESOID X-ACTIVATED RECEPTOR, FARNESOL RECEPTOR HRR-1, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP H MEMBER 4, RETINOID X RECEPTOR-INTERACTING PROTEIN 14, RXR-INTERACTING PROTEIN 14
 
Molecule 2 - ACTIVATOR PEPTIDE
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
17081Ligand/Ion3-[(E)-2-(2-CHLORO-4-{[3-{[(R)-(2,6-DICHLOROPHENYL)(HYDROXY)-LAMBDA~4~-SULFANYL]METHYL}-5-(1-METHYLETHYL)ISOXAZOL-4-YL]METHOXY}PHENYL)ETHENYL]BENZOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:265 , THR A:288 , MET A:290 , HIS A:294 , MET A:328 , PHE A:329 , ARG A:331 , SER A:332 , ILE A:335 , TYR A:361 , TYR A:369 , HIS A:447 , TRP A:454 , PHE A:461 , TRP A:469BINDING SITE FOR RESIDUE 708 A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GD2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GD2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GD2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GD2)

(-) Exons   (0, 0)

(no "Exon" information available for 3GD2)

(-) 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:227
 aligned with NR1H4_HUMAN | Q96RI1 from UniProtKB/Swiss-Prot  Length:486

    Alignment length:247
                                   249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       
          NR1H4_HUMAN   240 GRDLRQVTSTTKSCREKTELTPDQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLCEIWDVQ 486
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g                  d2A00 A:244-472 Retinoid X Recep tor                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------hhhhhhhhhhhhhhhhh...hhhhhhhhh...-hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh-....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gd2 A 244 GS------------------TPDQQTLLHFIMDSYNKQRMPQEITNKILKEE-SAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNK-LPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFAELLGRLTELRTFNHHHAEMLMSWRVNDHKFTPLLEEIWDVQ 472
                             |       -         -|      255       265       275 | |   285       295       305       315       325       335  | |  345       355       365       375       385       395       405       415       425       435       445       455       465       
                             |                246                            277 |                                                        338 |                                                                                                                                    
                           245                                                 279                                                          340                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 3gd2 B 745 AHQLLRYLLDA 755
                                   754 

   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  (0, 0)

(no "SCOP Domain" information available for 3GD2)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GD2)

(-) Gene Ontology  (66, 66)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NR1H4_HUMAN | Q96RI1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    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:0032052    bile acid binding    Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0038181    bile acid receptor activity    Combining with a bile acid and transmitting the signal to initiate a change in cell activity. A bile acid is any member of a group of steroid carboxylic acids occurring in bile.
    GO:1902122    chenodeoxycholic acid binding    Interacting selectively and non-covalently with chenodeoxycholic acid.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0046965    retinoid X receptor binding    Interacting selectively and non-covalently with a retinoid X receptor.
    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:0004887    thyroid hormone receptor activity    Combining with thyroid hormone 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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0015721    bile acid and bile salt transport    The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0008206    bile acid metabolic process    The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
    GO:0038183    bile acid signaling pathway    A series of molecular signals initiated by the binding of a bile acid to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0071398    cellular response to fatty acid    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 a fatty acid stimulus.
    GO:0071417    cellular response to organonitrogen 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 organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
    GO:0035356    cellular triglyceride homeostasis    Any process involved in the maintenance of an internal steady state of triglyceride within a cell or between a cell and its external environment.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0034971    histone H3-R17 methylation    The modification of histone H3 by addition of a methyl group to arginine at position 17 of the histone.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0072615    interleukin-17 secretion    The regulated release of any member of the interleukin-17 family of cytokines from a cell.
    GO:0038185    intracellular bile acid receptor signaling pathway    A series of molecular signals initiated by a bile acid binding to an receptor located within a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0043124    negative regulation of I-kappaB kinase/NF-kappaB signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling.
    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:0070858    negative regulation of bile acid biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.
    GO:1902714    negative regulation of interferon-gamma secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interferon-gamma secretion.
    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:1904468    negative regulation of tumor necrosis factor secretion    Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor secretion.
    GO:0001080    nitrogen catabolite activation of transcription from RNA polymerase II promoter    A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
    GO:2001250    positive regulation of ammonia assimilation cycle    Any process that activates or increases the frequency, rate or extent of ammonia assimilation cycle.
    GO:2000213    positive regulation of glutamate metabolic process    Any process that activates or increases the frequency, rate or extent of glutamate metabolic process.
    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:0070857    regulation of bile acid biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids.
    GO:0006109    regulation of carbohydrate metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates.
    GO:0090181    regulation of cholesterol metabolic process    Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving 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:0061178    regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:0010988    regulation of low-density lipoprotein particle clearance    Any process that modulates the rate, frequency or extent of low-density lipoprotein particle clearance. Low-density lipoprotein particle clearance is the process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0034255    regulation of urea metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving urea.
    GO:0009749    response to glucose    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 glucose stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    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:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0034142    toll-like receptor 4 signaling pathway    Any series of molecular signals generated as a consequence of binding to toll-like receptor 4.
    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.
cellular component
    GO:0005719    nuclear euchromatin    The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
    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
        NR1H4_HUMAN | Q96RI11osh 1osk 3bej 3dct 3dcu 3fli 3fxv 3hc5 3hc6 3l1b 3okh 3oki 3olf 3omk 3omm 3oof 3ook 3p88 3p89 3rut 3ruu 3rvf 4oiv 4qe6 4qe8 4wvd 5iaw 5ick 5q0i 5q0j 5q0k 5q0l 5q0m 5q0n 5q0o 5q0p 5q0q 5q0r 5q0s 5q0t 5q0u 5q0v 5q0w 5q0x 5q0y 5q0z 5q10 5q11 5q12 5q13 5q14 5q15 5q16 5q17 5q18 5q19 5q1a 5q1b 5q1c 5q1d 5q1e 5q1f 5q1g 5q1h 5q1i

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