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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PREGNANE X RECEPTOR BOUND TO COLUPULONE
 
Authors :  D. G. Teotico, J. Bischof, M. R. Redinbo
Date :  19 Jul 07  (Deposition) - 29 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha Helical Sandwhich, Protein-Ligand Complex, Alternative Splicing, Dna-Binding, Metal-Binding, Nucleus, Polymorphism, Receptor, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. G. Teotico, J. Bischof, M. R. Redinbo
Crystal Structure Of The Pregnane X Receptor Bound To Colupulone
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ORPHAN NUCLEAR RECEPTOR PXR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System VectorPRSET-A
    Expression System Vector TypePLASMID
    FragmentPXR LIGAND BINDING DOMAIN;
RESIDUES 130-434
    GeneNR1I2, PXR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymPREGNANE X RECEPTOR, ORPHAN NUCLEAR RECEPTOR PAR1, STEROID AND XENOBIOTIC RECEPTOR, SXR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CDZ1Ligand/Ion3,5-DIHYDROXY-4,6,6-TRIS(3-METHYLBUT-2-EN-1-YL)-2-(2-METHYLPROPANOYL)CYCLOHEXA-2,4-DIEN-1-ONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CDZ2Ligand/Ion3,5-DIHYDROXY-4,6,6-TRIS(3-METHYLBUT-2-EN-1-YL)-2-(2-METHYLPROPANOYL)CYCLOHEXA-2,4-DIEN-1-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:209 , MET A:243 , SER A:247 , GLN A:285 , PHE A:288 , MET A:323 , HIS A:407 , ARG A:410 , LEU A:411 , ILE A:414 , HOH A:445BINDING SITE FOR RESIDUE CDZ A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018341R148QNR1I2_HUMANPolymorphism  ---AR148Q
2UniProtVAR_033238A370TNR1I2_HUMANPolymorphism35761343AA370T
3UniProtVAR_018342R381WNR1I2_HUMANPolymorphism  ---AR381W
4UniProtVAR_018343I403VNR1I2_HUMANPolymorphism  ---AI403V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018341R148QNR1I2_HUMANPolymorphism  ---AR148Q
2UniProtVAR_033238A370TNR1I2_HUMANPolymorphism35761343AA370T
3UniProtVAR_018342R381WNR1I2_HUMANPolymorphism  ---AR381W
4UniProtVAR_018343I403VNR1I2_HUMANPolymorphism  ---AI403V

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QNV)

(-) Exons   (6, 6)

Asymmetric Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003937161aENSE00001516304chr3:119499331-1195011471817NR1I2_HUMAN-00--
1.3ENST000003937163ENSE00002156756chr3:119526076-119526294219NR1I2_HUMAN1-66660--
1.4aENST000003937164aENSE00000967516chr3:119528908-119529041134NR1I2_HUMAN66-111460--
1.5bENST000003937165bENSE00000967517chr3:119530386-119530573188NR1I2_HUMAN111-173631A:142-17332
1.6aENST000003937166aENSE00000967518chr3:119531533-119531807275NR1I2_HUMAN174-265921A:174-265 (gaps)92
1.7ENST000003937167ENSE00001149974chr3:119533826-119533968143NR1I2_HUMAN265-313491A:265-30945
1.8ENST000003937168ENSE00000967520chr3:119534170-119534286117NR1I2_HUMAN313-352401A:316-35237
1.9ENST000003937169ENSE00000967521chr3:119534573-119534678106NR1I2_HUMAN352-387361A:352-38736
1.10bENST0000039371610bENSE00001945549chr3:119535915-1195373321418NR1I2_HUMAN387-434481A:387-43448

(-) Sequences/Alignments

Asymmetric 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:249
 aligned with NR1I2_HUMAN | O75469 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:293
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431   
          NR1I2_HUMAN   142 GLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGS 434
               SCOP domains d2qnva_ A: Pregnane x receptor, PXR                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2qnvA00 A:142-434 Retinoid X Recepto                               r                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------                               --------------Hormone       _recep-2qnvA01 A:223-426                                                                                                                                                                      -------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...............-------------------------------..eeeeee.....eeee....-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee....eeee..eeeee.------.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------Q-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T----------W---------------------V------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b  PDB: A:142-173       Exon 1.6a  PDB: A:174-265 (gaps) UniProt: 174-265                                           -----------------------------------------------Exon 1.8  PDB: A:316-352 [INCOMPLETE]   ----------------------------------Exon 1.10b  PDB: A:387-434 UniProt: 387-434      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:265-309 UniProt: 265-313        --------------------------------------Exon 1.9  PDB: A:352-387            ----------------------------------------------- Transcript 1 (2)
                 2qnv A 142 GLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGV-------------------------------LKVSLQLRGEDGSVWNYKPPA-------FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLE------QQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGS 434
                                   151       161       171     |   -         -         -       211       221       | -     | 241       251       261       271       281       291       301       | -    |  321       331       341       351       361       371       381       391       401       411       421       431   
                                                             177                             209                 229     237                                                                     309    316                                                                                                                      

   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 Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (NR1I2_HUMAN | O75469)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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: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:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region 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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0046618    drug export    The directed movement of a drug, a substance used in the diagnosis, treatment or prevention of a disease, out of a cell or organelle.
    GO:0042738    exogenous drug catabolic process    The chemical reactions and pathways resulting in the breakdown of a drug that has originated externally to the cell or organism.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010628    positive regulation of gene expression    Any process that increases 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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    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:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
    GO:0042908    xenobiotic transport    The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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
        NR1I2_HUMAN | O754691ilg 1ilh 1m13 1nrl 1skx 2o9i 3ctb 3hvl 3r8d 4j5w 4j5x 4ny9 4s0s 4s0t 4x1f 4x1g 4xao 4xhd 5a86

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QNV)