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(-) Description

Title :  STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM FOR A SET OF CHEMICALLY RELATED PROGESTERONE RECEPTOR MODULATORS
 
Authors :  S. J. Lusher, H. C. A. Raaijmakers, D. Vu-Pham, K. Dechering, T. Wai Lam A. R. Brown, N. M. Hamilton, O. Nimz, R. Azevedo, R. Mcguire, A. Oubrie, J. De Vlieg
Date :  15 Jun 11  (Deposition) - 17 Aug 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Receptor, Agonist, Antagonist (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. W. Lam, A. R. Brown, N. M. Hamilton, O. Nimz, R. Bosch, R. Mcguire, A. Oubrie, J. De Vlieg
Structural Basis For Agonism And Antagonism For A Set Of Chemically Related Progesterone Receptor Modulators.
J. Biol. Chem. V. 286 35079 2011
PubMed-ID: 21849509  |  Reference-DOI: 10.1074/JBC.M111.273029

(-) Compounds

Molecule 1 - PROGESTERONE RECEPTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentLIGAND BINDING DOMAIN, RESIDUES 678-933
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2OR81Ligand/Ion2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE
3ORC1Ligand/Ion(R)-N-[1-[4-(3,5-DIMETHYLISOXAZOL-4-YL) PHENYL]ETHYL]-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2OR81Ligand/Ion2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE
3ORC-1Ligand/Ion(R)-N-[1-[4-(3,5-DIMETHYLISOXAZOL-4-YL) PHENYL]ETHYL]-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2OR8-1Ligand/Ion2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE
3ORC1Ligand/Ion(R)-N-[1-[4-(3,5-DIMETHYLISOXAZOL-4-YL) PHENYL]ETHYL]-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:715 , LEU A:718 , ASN A:719 , LEU A:721 , GLN A:725 , MET A:756 , MET A:759 , MET A:801 , CYS A:891 , THR A:894BINDING SITE FOR RESIDUE OR8 A1000
2AC2SOFTWARELEU B:715 , LEU B:718 , ASN B:719 , TRP B:755 , MET B:756 , MET B:759 , MET B:801 , TYR B:890 , CYS B:891 , PHE B:905 , MET B:909BINDING SITE FOR RESIDUE ORC B1000
3AC3SOFTWAREPRO A:737 , GLY A:738 , ARG A:740 , ASN A:741 , HOH A:2138 , PRO B:737 , GLY B:738 , ARG B:740 , ASN B:741BINDING SITE FOR RESIDUE SO4 A1933
4AC4SOFTWAREPRO A:737 , GLY A:738 , MET A:844 , SER A:847 , GOL A:1936BINDING SITE FOR RESIDUE GOL A1934
5AC5SOFTWARETYR A:753 , THR A:829 , HIS A:881 , HIS A:888 , ILE A:920 , HOH A:2050 , HOH A:2114BINDING SITE FOR RESIDUE GOL A1935
6AC6SOFTWAREGOL A:1934 , HOH A:2138 , LEU B:687 , GLY B:738 , SER B:847BINDING SITE FOR RESIDUE GOL A1936
7AC7SOFTWARETYR B:890 , ASN B:893 , THR B:894BINDING SITE FOR RESIDUE GOL B1933

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014628S865LPRGR_HUMANPolymorphism2020880A/BS865L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014628S865LPRGR_HUMANPolymorphism2020880AS865L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014628S865LPRGR_HUMANPolymorphism2020880BS865L

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003254551aENSE00001204729chr11:101001255-1009981653091PRGR_HUMAN1-5465460--
1.2ENST000003254552ENSE00000989714chr11:100996889-100996738152PRGR_HUMAN546-597520--
1.3ENST000003254553ENSE00000745002chr11:100962607-100962491117PRGR_HUMAN597-636400--
1.4bENST000003254554bENSE00000795216chr11:100933483-100933178306PRGR_HUMAN636-7381032A:683-738
B:683-738
56
56
1.5aENST000003254555aENSE00000989716chr11:100922299-100922155145PRGR_HUMAN738-786492A:738-786
B:738-786
49
49
1.6aENST000003254556aENSE00000989717chr11:100920790-100920660131PRGR_HUMAN786-830452A:786-830
B:786-830
45
45
1.7aENST000003254557aENSE00000795215chr11:100912833-100912676158PRGR_HUMAN830-882532A:830-882
B:830-882
53
53
1.8dENST000003254558dENSE00001350778chr11:100910002-1009003559648PRGR_HUMAN883-933512A:883-932
B:883-932
50
50

(-) 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:250
 aligned with PRGR_HUMAN | P06401 from UniProtKB/Swiss-Prot  Length:933

    Alignment length:250
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932
           PRGR_HUMAN   683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
               SCOP domains d3zrba_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeehhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: A:683-738 UniProt: 636-738 [INCOMPLETE] -----------------------------------------------Exon 1.6a  PDB: A:786-830 UniProt: 786-830   ----------------------------------------------------Exon 1.8d  PDB: A:883-932 UniProt: 883-933         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.5a  PDB: A:738-786 UniProt: 738-786       -------------------------------------------Exon 1.7a  PDB: A:830-882 UniProt: 830-882           -------------------------------------------------- Transcript 1 (2)
                 3zrb A 683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with PRGR_HUMAN | P06401 from UniProtKB/Swiss-Prot  Length:933

    Alignment length:250
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932
           PRGR_HUMAN   683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
               SCOP domains d3zrbb_ B: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeehhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4b  PDB: B:683-738 UniProt: 636-738 [INCOMPLETE] -----------------------------------------------Exon 1.6a  PDB: B:786-830 UniProt: 786-830   ----------------------------------------------------Exon 1.8d  PDB: B:883-932 UniProt: 883-933         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------Exon 1.5a  PDB: B:738-786 UniProt: 738-786       -------------------------------------------Exon 1.7a  PDB: B:830-882 UniProt: 830-882           -------------------------------------------------- Transcript 1 (2)
                 3zrb B 683 LIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHK 932
                                   692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZRB)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRGR_HUMAN | P06401)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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: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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0005496    steroid binding    Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0010629    negative regulation of gene expression    Any process that decreases 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: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: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: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:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    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.
    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
        PRGR_HUMAN | P064011a28 1e3k 1sqn 1sr7 1zuc 2c7a 2ovh 2ovm 2w8y 3d90 3g8o 3hq5 3kba 3zr7 3zra 4a2j 4apu 4oar 5cc0

(-) Related Entries Specified in the PDB File

1a28 HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN
1e3k HUMAN PROGESTERON RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITH THE LIGAND METRIBOLONE (R1881)
1sqn PROGESTERONE RECEPTOR LIGAND BINDING DOMAIN WITH BOUNDNORETHINDRONE
1sr7 PROGESTERONE RECEPTOR HORMONE BINDING DOMAIN WITH BOUNDMOMETASONE FUROATE
1zuc PROGESTERONE RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITHTHE NONSTEROIDAL AGONIST TANAPROGET
2c7a STRUCTURE OF THE PROGESTERONE RECEPTOR-DNA COMPLEX
2w8y RU486 BOUND TO THE PROGESTERONE RECEPTOR IN A DESTABILIZED AGONISTIC CONFORMATION
3zr7 STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM FOR A SET OF CHEMICALLY RELATED PROGESTERONE RECEPTOR MODULATORS
3zra STRUCTURAL BASIS FOR AGONISM AND ANTAGONISM FOR A SET OF CHEMICALLY RELATED PROGESTERONE RECEPTOR MODULATORS