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(-) Description

Title :  GR DNA BINDING DOMAIN:FKBP5 COMPLEX-52, 18BP
 
Authors :  M. A. Pufall, K. R. Yamamoto, S. H. Meijsing
Date :  08 Feb 09  (Deposition) - 21 Apr 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Glucocorticoid, Dna-Binding, Allostery, Lever Arm, Transcription, Hormone, Alternative Initiation, Chromatin Regulator, Cytoplasm, Lipid-Binding, Metal-Binding, Nucleus, Phosphoprotein, Polymorphism, Receptor, Steroid- Binding, Transcription Regulation, Ubl Conjugation, Zinc, Zinc-Finger, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. H. Meijsing, M. A. Pufall, A. Y. So, D. L. Bates, L. Chen, K. R. Yamamoto
Dna Binding Site Sequence Directs Glucocorticoid Receptor Structure And Activity.
Science V. 324 407 2009
PubMed-ID: 19372434  |  Reference-DOI: 10.1126/SCIENCE.1164265
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*TP*G)- 3')
    ChainsC
    EngineeredYES
    Other DetailsFKBP5 BINDING SITE TOP STRAND 18BP
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*TP*G)- 3')
    ChainsD
    EngineeredYES
    Other DetailsFKBP5 BINDING SITE BOTTOM STRAND 18BP
    SyntheticYES
 
Molecule 3 - GLUCOCORTICOID RECEPTOR
    ChainsB, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3) GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 440-525
    GeneGRL, NR3C1
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymGR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:440 , CYS B:443 , CYS B:457 , CYS B:460BINDING SITE FOR RESIDUE ZN B1514
2AC2SOFTWARECYS B:476 , CYS B:482 , CYS B:492 , CYS B:495BINDING SITE FOR RESIDUE ZN B1515
3AC3SOFTWARECYS A:440 , CYS A:443 , CYS A:457 , CYS A:460BINDING SITE FOR RESIDUE ZN A1512
4AC4SOFTWARECYS A:476 , CYS A:482 , CYS A:492 , CYS A:495BINDING SITE FOR RESIDUE ZN A1513

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G6R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G6R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G6R)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEAR_REC_DBD_2PS51030 Nuclear hormone receptors DNA-binding domain profile.GCR_RAT437-512
 
  2A:440-512
B:440-510
2NUCLEAR_REC_DBD_1PS00031 Nuclear hormones receptors DNA-binding region signature.GCR_RAT440-466
 
  2A:440-466
B:440-466

(-) Exons   (0, 0)

(no "Exon" information available for 3G6R)

(-) 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:79
 aligned with GCR_RAT | P06536 from UniProtKB/Swiss-Prot  Length:795

    Alignment length:79
                                   446       456       466       476       486       496       506         
              GCR_RAT   437 PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKK 515
               SCOP domains d3g6ra_ A: automated matches                                                    SCOP domains
               CATH domains 3g6rA00 A:437-515 Erythroid Transcription Factor GATA-1, subunit A              CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeehhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUCLEAR_REC_DBD_2  PDB: A:440-512 UniProt: 437-512                          --- PROSITE (1)
                PROSITE (2) ---NUCLEAR_REC_DBD_1          ------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------- Transcript
                 3g6r A 437 SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKK 515
                                   446       456       466       476       486       496       506         

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with GCR_RAT | P06536 from UniProtKB/Swiss-Prot  Length:795

    Alignment length:74
                                   446       456       466       476       486       496       506    
              GCR_RAT   437 PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEAR 510
               SCOP domains d3g6rb_ B: automated matches                                               SCOP domains
               CATH domains 3g6rB00 B:437-510 Erythroid Transcription Factor GATA-1, subunit A         CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeehhhhhhhhhhhhhhh....................hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUCLEAR_REC_DBD_2  PDB: B:440-510 UniProt: 437-512                         PROSITE (1)
                PROSITE (2) ---NUCLEAR_REC_DBD_1          -------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------- Transcript
                 3g6r B 437 SHMCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEAR 510
                                   446       456       466       476       486       496       506    

Chain C from PDB  Type:DNA  Length:18
                                                  
                 3g6r C   1 CCAGAACAGGGTGTTCTG  18
                                    10        

Chain D from PDB  Type:DNA  Length:18
                                                  
                 3g6r D   1 CCAGAACACCCTGTTCTG  18
                                    10        

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G6R)

(-) Gene Ontology  (71, 71)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GCR_RAT | P06536)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030544    Hsp70 protein binding    Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
    GO:0051879    Hsp90 protein binding    Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
    GO:0001012    RNA polymerase II regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0004883    glucocorticoid receptor activity    Combining with a glucocorticoid and transmitting the signal within the cell trigger a change in cell activity or function.
    GO:0038051    glucocorticoid-activated RNA polymerase II transcription factor binding transcription factor activity    Combining with a glucocorticoid and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. For example, glucocorticoid-bound receptors can bind to transcription factor complexes to regulate transcription of genes whose promoters do not contain glucocorticoid response elements.
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0042562    hormone binding    Interacting selectively and non-covalently with any hormone, naturally occurring substances secreted by specialized cells that affect the metabolism or behavior of other cells possessing functional receptors for the hormone.
    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: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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase 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: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:1990239    steroid hormone binding    Interacting selectively and non-covalently with a steroid hormone.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0008209    androgen metabolic process    The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0071549    cellular response to dexamethasone stimulus    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 dexamethasone stimulus.
    GO:0071286    cellular response to magnesium ion    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 magnesium ion stimulus.
    GO:0071383    cellular response to steroid hormone stimulus    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 steroid hormone stimulus.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0048096    chromatin-mediated maintenance of transcription    Maintenance of transcription by remodelling of chromatin into an 'open configuration'. Once established, this regulation is mitotically stable and is maintained over many cell divisions. It is also heritable.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0043402    glucocorticoid mediated signaling pathway    A series of molecular signals mediated by the detection of a glucocorticoid hormone.
    GO:0042921    glucocorticoid receptor signaling pathway    Any series of molecular signals generated as a consequence of a glucocorticoid binding to its receptor.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0014889    muscle atrophy    A process, occurring in the muscle, that is characterized by a decrease in protein content, fiber diameter, force production and fatigue resistance in response to different conditions such as starvation, aging and disuse.
    GO:0031914    negative regulation of synaptic plasticity    A process that decreases synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0043116    negative regulation of vascular permeability    Any process that reduces the extent to which blood vessels can be pervaded by fluid.
    GO:0061051    positive regulation of cell growth involved in cardiac muscle cell development    Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
    GO:0060999    positive regulation of dendritic spine development    Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:2000324    positive regulation of glucocorticoid receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of glucocorticoid receptor signaling pathway.
    GO:0014049    positive regulation of glutamate secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of glutamate.
    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:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0010906    regulation of glucose metabolic process    Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0014823    response to activity    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 activity stimulus.
    GO:0046685    response to arsenic-containing substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
    GO:0051592    response to calcium ion    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 calcium ion stimulus.
    GO:0051412    response to corticosterone    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 corticosterone stimulus. Corticosterone is a 21 carbon steroid hormone of the corticosteroid type, produced in the cortex of the adrenal glands. In many species, corticosterone is the principal glucocorticoid, involved in regulation of fuel metabolism, immune reactions, and stress responses.
    GO:0071548    response to dexamethasone    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 dexamethasone stimulus.
    GO:0051602    response to electrical stimulus    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 electrical stimulus.
    GO:0014854    response to inactivity    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 inactivity stimulus.
    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:0046689    response to mercury ion    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 mercury ion stimulus.
    GO:0009314    response to radiation    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 electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    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:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GCR_RAT | P065361gdc 1glu 1lat 1r4o 1r4r 1rgd 2gda 3fyl 3g6p 3g6q 3g6t 3g6u 3g8u 3g8x 3g97 3g99 3g9i 3g9j 3g9m 3g9o 3g9p

(-) Related Entries Specified in the PDB File

3fyl SAME PROTEIN, DIFFERENT DNA
3g6p SAME COMPLEX, DIFFERENT CRYSTAL CONDITION
3g6q SAME DNA BINDING SITE, INSERTION MUTATION GR GAMMA
3g6t
3g6u
3g8x
3g97